Peripheral blood dna methylation models as predictors of knee osteoarthritis radiographic progression

ABSTRACT

The present invention includes a method for determining whether a subject diagnosed with osteoarthritis is at increased risk for progression to severe osteoarthritis within 12-24 months, the method comprising the steps of: (a) preparing a blood sample; (b) measuring in the blood sample prepared in step (a) a level of DNA methylation; (c) comparing the DNA methylation level(s) measured in step (b) to a control blood sample level(s) of DNA methylation, and (d) identifying the subject as being at increased risk for progression to severe osteoarthritis within 12-24 months when the DNA methylation is increased by at least 2 fold as compared to the control blood level(s) of DNA methylation.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority based on U.S. Provisional Application No. 63/112,973, filed Nov. 12, 2021. The contents of which is incorporated by reference in its entirety.

STATEMENT OF FEDERALLY FUNDED RESEARCH

This invention was made with government support under K08-AR070891 and P30-AR053483 awarded by the National Institutes of Health. The government has certain rights in the invention.

TECHNICAL FIELD OF THE INVENTION

The present invention relates in general to the field of peripheral blood DNA methylation, and more particularly, a novel method of predicting knee osteoarthritis radiographic progression from peripheral blood DNA methylation.

BACKGROUND OF THE INVENTION

Without limiting the scope of the invention, its background is described in connection with Knee osteoarthritis (OA).

Osteoarthritis (OA) is the leading cause of chronic disability in the United States, and is the third most rapidly rising chronic medical condition associated with disability worldwide [1,2]. Despite its importance and economic impact, there are no disease-modifying anti-osteoarthritic drugs (DMOADs) approved by the US Food and Drug Administration (FDA) or European Medicines Agency, in stark contrast to the multitude of biologic and nonbiologic disease-modifying treatments available in other forms of arthritis [3]. This lag in the development of DMOADs is due in no small part to a lack of easily accessible radiographic and/or biochemical biomarkers to diagnose OA and discriminate patient phenotypes, including prediction of future progressors.

Accordingly, much attention has recently been focused on the development of diagnostic and prognostic biomarkers for OA. Several groups have described biomarker candidates for OA diagnosis, discriminating OA patients from healthy controls based on peripheral blood analytes. In 2014, Ramos et al. described an mRNA-based peripheral blood signature which could discriminate OA patients from matched controls [4], with a c-statistic of 0.97. In 2018, Li et al. published a reanalysis of these data using a different machine learning technique that performed at an equally high sensitivity and specificity on a reduced subset genes [5]. In 2018, Huang and colleagues used data and biospecimens from the DOXY (doxycycline for treatment of OA) clinical trial to examine four plasma biomarkers [6] and found baseline levels of lipopolysaccharide binding protein (LBP) were associated with future radiographic progression (TIC over 18 months OR=1.418).

A more difficult but perhaps more clinically relevant biomarker task, however, is the classification of OA patients into distinct phenotypes. The largest study yet to take on the task of OA phenotype discrimination was an analysis of serum and urine biochemical biomarkers performed by the Foundation for the National Institutes of Health (FNIH) OA Biomarkers Consortium (OABC-FNIH), using data and biospecimens from the longitudinal, US-based Osteoarthritis Initiative (OAI) study [7,8]. In this study, the authors produced a model combining three serum and urine biomarkers that could discriminate radiographic and pain progressors from nonprogressors with a receiver operator characteristic area under the curve (AUC-ROC, c-statistic) of 0.631[9]. Baseline values of these parameters did not offer substantial predictive capability; rather, models utilized a time-integrated concentration (TIC) approach tracking analyte measurements over a period of years.

A drawback of traditional biochemical biomarkers such as those used in the OABC-FNIH is their inherent variability. Epigenetic assays offer theoretical advantages as biomarkers. Most notably, an epigenetics-based assay has the potential to offer prognostic information based on a single time point reflecting early, relatively stable gene regulatory changes that precede gene transcription and subsequent protein translation. Early epigenetic changes in peripheral blood have been found to be useful biomarkers in several rheumatic diseases including rheumatoid arthritis [10] and systemic lupus erythematosus [11], as well as several chronic low-level inflammatory diseases, including type-2 diabetes mellitus risk [12] and cardiovascular disease [13]. Several recent studies, including our own, have demonstrated alterations in joint tissue epigenetic patterns associated with OA development and progression [14-18]; however, no analyses of blood epigenetic changes have yet been published.

Despite these advances, what is needed is a rapid, inexpensive, and widely available method and system to identify OA disease progression from easily accessible biological samples.

SUMMARY OF THE INVENTION

In one embodiment, the present invention includes a method for determining whether a subject diagnosed with osteoarthritis is at increased risk for progression to severe osteoarthritis within 12-24 months, the method comprising the steps of: (a) preparing a blood sample; (b) measuring in the blood sample prepared in step (a) a level of DNA methylation, e.g., by differentiation of bisulfite-generated polymorphisms; (c) comparing the DNA methylation level(s) measured in step (b) to a control blood sample level(s) of DNA methylation in a subject without osteoarthritis, and (d) identifying the subject as being at increased risk for progression to severe osteoarthritis within 12-24 months when the DNA methylation is increased by at least 2 fold as compared to the control blood level(s) of DNA methylation. In one aspect, the blood sample comprises peripheral blood mononuclear cells or cell-free DNA. In another aspect, the control blood level of the DNA methylation in a similarly processed blood sample from a control subject or a mean level of several control subjects. In another aspect, the control subject (i) is matched to the tested subject by at least one of: age category, sex, BMI category, ethnicity, or baseline KL radiographic grade; and (ii) does not have osteoarthritis as determined by both radiographic and symptomatic examination. In another aspect, the control blood level of the DNA methylation is a predetermined standard. In another aspect, the DNA methylation is determined with a 450k, or 850k array, or CpG sites associates with at least one of: an antigen presentation pathway, adenosine monophosphate kinase (AMPK) signaling pathway, or a sonic hedgehog signaling pathway, or one or more top upstream regulators identified by IPA selected from transcription factor PITX2, histone H3, histone H4, miR-141, miR-9, miR-137, bone morphogenic protein 2, a TGF-β superfamily member, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 markers selected from cg04195161, cg22064129, cg04985016, cg12692919, cg04043957, cg08872579, cg02019955, cg01333532, cg23705082, cg05042110, cg00715363, cg01307007 and cg09239099. In another aspect, the subject is human. In another aspect, the osteoarthritis is a knee osteoarthritis. In another aspect, the subject has a Kellgren-Lawrence (KL) score of 1-3 in at least one knee. In another aspect, the method further comprises the step of treating the osteoarthritis wherein the treatment is at least one of acetaminophen, steroids, hyaluronic acid, nonsteroidal anti-inflammatory drugs (NSAIDs), or Duloxetine.

In another embodiment, the present invention includes a method for treating osteoarthritis in a subject, wherein the subject has been diagnosed with osteoarthritis but does not have severe osteoarthritis, the method comprising the steps of: (a) measuring in a blood plasma sample obtained from the subject the plasma level of DNA methylation, e.g., by differentiation of bisulfite-generated polymorphisms; and (b) if the plasma level DNA methylation is increased by at least 2 fold as compared to a control plasma level(s) of the DNA methylation in a subject without osteoarthritis, administering an osteoarthritis treatment to the subject. In one aspect, the subject has been diagnosed with knee osteoarthritis and has a Kellgren-Lawrence (KL) score of 1-3 in at least one knee. In another aspect, the subject is human. In another aspect, the blood plasma sample obtained from the subject has been prepared in the presence of heparin. In another aspect, the DNA methylation is determined with a 450k, or 850k array, or CpG sites associates with at least one of: an antigen presentation pathway, adenosine monophosphate kinase (AMPK) signaling pathway, or a sonic hedgehog signaling pathway, or one or more top upstream regulators identified by IPA selected from transcription factor PITX2, histone H3, histone H4, miR-141, miR-9, miR-137, bone morphogenic protein 2, a TGF-β superfamily member, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 markers selected from cg04195161, cg22064129, cg04985016, cg12692919, cg04043957, cg08872579, cg02019955, cg01333532, cg23705082, cg05042110, cg00715363, cg01307007 and cg09239099. In another aspect, the control blood level of the DNA methylation is a level of DNA methylation in a similarly processed blood sample from a control subject or a mean level of several control subjects. In another aspect, the control subject (i) is matched to the tested subject by at least one of: age category, sex, BMI category, ethnicity, or baseline KL radiographic grade; and (ii) does not have osteoarthritis as determined by both radiographic and symptomatic examination. In another aspect, the control plasma level of the DNA methylation is a predetermined standard. In another aspect, the osteoarthritis treatment is at least one of acetaminophen, steroids, hyaluronic acid, nonsteroidal anti-inflammatory drugs (NSAIDs), or Duloxetine.

In another embodiment, the present invention includes a method for treating osteoarthritis in a subject, the method comprising administering an osteoarthritis treatment to a subject with elevated plasma levels of DNA methylation, wherein the subject does not have severe osteoarthritis. In one aspect, the subject has been diagnosed with knee osteoarthritis and has a Kellgren-Lawrence (KL) score of 1-3 in at least one knee. In another aspect, the subject is human. In another aspect, the osteoarthritis treatment is at least one of acetaminophen, steroids, hyaluronic acid, nonsteroidal anti-inflammatory drugs (NSAIDs), or Duloxetine.

BRIEF DESCRIPTION OF THE DRAWINGS

For a more complete understanding of the features and advantages of the present invention, reference is now made to the detailed description of the invention along with the accompanying figures and in which:

FIG. 1 is a graph that shows the mean receiver operator characteristic (ROC) curves for patient characteristic-only models, DNA methylation-based models using Beta values, and DNA methylation-based models using M values models when tested on previously untested samples. Curves represent mean values over 40 cycles of development, error bars represent SEM. ROC-AUC (c-statistic) values are given as mean±SEM.

FIG. 2 is a flowchart that shows the Osteoarthritis (OA) rapid progressor PBMC DNA methylation-based machine learning discriminant model development plan.

FIG. 3 is a graph that shows a model performance by number of CpG sites included during development, including the mean number of CpGs selected for inclusion during model development and optimization was 22±2 (mean±SEM) for M-based and 19±2 for beta value-based assays.

FIG. 4 is a flowchart that shows another Osteoarthritis (OA) rapid progressor PBMC DNA methylation-based machine learning discriminant model development plan.

DETAILED DESCRIPTION OF THE INVENTION

While the making and using of various embodiments of the present invention are discussed in detail below, it should be appreciated that the present invention provides many applicable inventive concepts that can be embodied in a wide variety of specific contexts. The specific embodiments discussed herein are merely illustrative of specific ways to make and use the invention and do not delimit the scope of the invention.

To facilitate the understanding of this invention, a number of terms are defined below. Terms defined herein have meanings as commonly understood by a person of ordinary skill in the areas relevant to the present invention. Terms such as “a”, “an” and “the” are not intended to refer to only a singular entity, but include the general class of which a specific example may be used for illustration. The terminology herein is used to describe specific embodiments of the invention, but their usage does not delimit the invention, except as outlined in the claims.

The present invention uses peripheral blood mononuclear cell (PBMC)-based epigenetic models to predict future knee OA radiographic progression in a well-matched cohort of patients from the Osteoarthritis Initiative (OAI), using similar definitions to those previously published in OABC-FNIH studies[9].

Baseline patient demographic, disease, and PBMC composition characteristics were well matched. Models developed using only patient characteristics were not predictive of future progression.

The inventors first identified a group of 58 OA radiographic progressors with baseline Kellergren-Lawrence (K/L) radiographic grade 2-3, symptomatic knee OA who exhibited ≥0.7 mm of joint space width (JSW) loss over the first 24 months of follow-up and persistent JSW loss at 48 months from the longitudinal, US-based Osteoarthritis Initiative (OAI) study. The inventors then matched 58 nonprogressors with ≤0.5 mm of joint space width loss over 48 months of follow-up by age category, sex, BMI category, ethnicity, and baseline KL radiographic grade (Table 1). Although not included in the initial matching criteria, there were no statistical differences in baseline JSW, NSAID use, or smoking history between the two groups. The inventors did note a statistically significant increase in baseline Western Ontario and McMaster (WOMAC) pain subscale among progressors (21.5±2 mean±SEM vs. 17.0±1.5 points on a 0-100 point normalized scale, P=0.05).

TABLE 1 Patient group characteristics Radiographic Nonprogressors 2- progressors (cases) (controls) tailed (n = 58), (n = 58), P mean ± SEM mean ± SEM value Baseline characteristics Age 60 ± 1    60 ± 1    0.90 Sex (% female) 53.4%   60.3%   0.13 BMI 30.5 ± 0.5    30.9 ± 0.6    0.61 Ethnicity (% Caucasian) 88% 88% 1.00 Smoking (% positive) 46% 43% 0.71 NSAID use (% positive) 29% 17% 0.13 Mean WOMAC pain (0- 21.5 ± 2    17.0 ± 1.5    0.05 100 point normalized scale) Mean JSW (mm) 3.9 ± 0.1  4.0 ± 0.1  0.34 Baseline K/L grade 2 25  35  0.09 Baseline K/L grade 3 33  23  Baseline estimated PBMC composition CD8+ T cells 8.5 ± 0.7% 8.6 ± 0.6% 0.9 CD4+ T cells  21 ± 0.9% 21 ± 1%  0.9 NK cells 7.4 ± 0.5% 7.6 ± 0.6% 0.9 B cells 9.6 ± 0.5% 9.8 ± 0.5% 0.8 Monocytes 7.4 ± 0.3% 6.7 ± 0.3% 0.12 Granulocytes 51 ± 1%  51 ± 1%  0.9 Baseline comorbidities Type 2 diabetes 4 (patients/58) 6 (# patients/58) 0.74 History of heart attack 0 0 n/a History of heart failure 2 3 1.0 History of stroke 2 4 0.68 History of lung disease 0 0 n/a History of cancer 1 4 0.36

Recent studies have reported that clinical characteristics alone can be used to model future GA progression[19]. To ensure that these models were not being affected by patient characteristics, the inventors first developed models using baseline patient characteristics data alone, without including DNA methylation data. These models included age, sex, BMI, baseline JSW, baseline WOMAC pain, smoking history, and NSAID use. Baseline models were not able to discriminate the two groups (receiver operator characteristic area under the curve ROC-AUC, c-statistic=0.49±0.01 mean±SEM, accuracy=50±0.7%) (FIG. 1). Although infrequent, the inventors then added data regarding comorbidities to these baseline models, including history of heart attack, heart failure, diabetes, lung disease, and cancer (Table 1). This did not improve the discriminatory capability of baseline patient characteristic models (p=0.28 for comparison with models not including comorbidity data).

DNA methylation data from mixed PBMC samples can be skewed by underlying differences in cellular composition among groups[20]. As the OAI dataset does not include data on individual blood sample cellular composition, the inventors estimated this using a computational approach[21]. There were no statistically significant differences in estimated PBMC composition between the two groups; however, the inventors did note a trend towards increased monocyte counts in cases (progressors 7.4±0.3% mean±SEM vs. nonprogressors 6.7±0.3%, P=0.12) (Table 1). Accordingly, the inventors corrected the dataset for PBMC composition differences using frozen surrogate variable analysis (FSVA), a technique previously demonstrated to be robust in correcting cellular composition differences in genome-wide DNA methylation data[22,23], before developing these epigenetic models.

Models developed based on PBMC DNA methylation data are predictive of radiographic progression. Traditionally, epigenome-wide association studies have reported DNA methylation data as beta values, defined as the fraction methylation (0-1 scale) of each CpG site included in the array. However, beta values are characterized by high heteroscedasticity (most beta values fall within extreme high- and low-percent methylation levels). Therefore, the inventors also analyzed M values (the log base-2 ratio of methylated:unmethylated probe intensities for a given CpG site), which are approximately homoscedastic, in these models[24]. In this analysis, models based on PBMC DNA methylation data were consistently capable of discriminating those patients who would go on to experience radiographic progression from nonprogressors (FIG. 1, FIG. 2, Table 2). Models based on M values outperformed those based on beta values (M value models c=0.81±0.01, mean±SEM, vs. beta value models 0.75±0.01, comparison p=0.002), with corresponding accuracies of 73±1%, mean±SEM, for M and 69±1% for beta based models. The mean number of CpGs selected for inclusion during model development and optimization was 22±2 (mean±SEM) for M-based and 19±2 for beta value-based assays (FIG. 3), this was not statistically significantly different between the two DNA methylation measures (p=0.32).

The inventors then added patient characteristic covariate data to model development, including age, sex, BMI, baseline JSW, baseline WOMAC pain, smoking history, and NSAID use. Including these data did not alter model performance (M value models c=0.80±0.01, beta value models c=0.78±0.01, both nonsignificant compared to models without covariates). Finally, as this analysis included data from two methylation assay types, the inventors then analyzed model performance for 450k and 850k chips separately; both types demonstrated equivalent performance in these models (p=0.27).

TABLE 2 Performance of PBMC DNA methylation models to predict future radiographic progression in OA patients when evaluating previously unseen data. M-value based models Beta value-based models (mean ± SEM) (mean ± SEM) ROC-AUC (c-statistic) 0.81 ± 0.01  0.75 ± 0.01  Accuracy 73 ± 1% 69 ± 1% Odds ratio 11 ± 2  9 ± 2  Sensitivity 74 ± 1% 73 ± 2% Specificity 70 ± 1% 70 ± 1%

A subset of DNA methylation CpG sites were selected frequently in multiple rounds of model development and were enriched in functional pathways previously associated with OA development. Although 969 CpGs were selected in at least one round of model development in either M or Beta based models, a subset of CpG sites were selected several times (Table 3, complete list of CpGs selected in Table 4). Many of these most frequently selected CpGs in both M value-based and Beta value-based model development were shared; for example, 7 of the top 20 most frequently selected CpGs in both M- and Beta-models were identical. The majority of the top 20 CpGs selected during modeling were associated with CpG islands (13 of 20 M- and 16 of 20 Beta-based models), including all but one of the CpG sites shared among the two methylation measures, suggesting these sites may play a role in gene regulation.

TABLE 3 Top 20 CpGs selected for supervised model development. CpGs shared by both Beta-value-based and M-value-based models are highlighted in bold (n = 7). M value- # of CpG Location Beta value- # of CpG Location based development location within based development location within algorithm rounds selected Associated (regulatory CpG algorithm rounds selected Associated (regulatory CpG feature (out of 40) gene region) island feature (out of 40) gene region) island cg15974085 15 C18orf55; TSS200 Island cg11865413 15 N _(—) Shelf FBXO15 cg26384229 14 ALG10B TSS200 Island cg21643086 15 cg21643086 12 cg17745251 11 C10orf140 Body Island cg03687650 11 OSBPL5 Body S _(—) Shelf cg06409741 11 RASA3 Body Island cg06409741 11 RASA3 Body Island cg03870777 10 KRT18 TSS200 N _(—) Shore cg18111500 10 cg17956079 10 PLEKHB1 TSS200 cg07772660 9 MST1P9 Body Island cg26384229 9 ALG10B TSS200 Island cg11865413 9 N _(—) Shelf cg03687650 7 OSBPL5 Body S _(—) Shelf cg03212634 9 cg10306485 7 RASAS Body S_Shelf cg00142933 8 LIMS2 Body N_Shore cg19559392 7 MORN2; 5′UTR; S_Shore DHX57 TSS1500 cg16001460 8 PRIM2 TSS1500 cg05587853 7 MSL2 TSS1500 Island cg17745251 7 C10orf140 Body Island cg14616423 7 cg14330460 7 cg08728848 6 cg03870777 6 KRT18 TSS200 N _(—) Shore cg07379140 5 ALG14 TSS200 Island cg02215141 6 gl N_Shore cg02962630 5 DLL4 Body Island cg20200361 6 THADA Body cg16790849 5 NEU1 Body N_Shore cg07258847 6 cg00143249 5 MNX1 Body Island cg23226134 5 CLCN6; 1st Exon Island cg10609068 4 ANO6 TSS1500; N_Shore MTHFR PLEKHA9 5′UTR cg16121685 5 UHMK1 TSS200 Island cg14710040 4 EEF2 TSS200 Island cg10966582 5 MST1P9 Body Island cg17310773 4 SLC25A17 1stExon Island

Although a differential methylation analysis was not performed in the traditional sense, it was reasoned that CpG sites chosen for inclusion in these models might still clustered in functional pathways important in OA. To investigate this, the inventors performed gene ontology analysis using the Ingenuity Pathway Analysis (IPA) system of genes associated with CpG sites chosen in at least one round of model development. The most significantly enriched canonical pathways enriched in this gene set included the antigen presentation pathway (n=6 genes, p=7E-4), adenosine monophosphate kinase (AMPK) signaling (n=15, p=1E-3, and sonic hedgehog signaling (n=4 genes, p=9E-3), among others (Table 4). The top upstream regulators identified by IPA include the transcription factor PITX2 (n=14 genes, p=1E-5), histone H3 (n=29 genes, p=7E-5) and H4 (n=14,p=9.6E-5), miR-141 (n=9, p=1.9E-4), miR-9 (n=5, p=3.4E-4), miR-137 (n=2, p=8.2E-4), and bone morphogenic protein 2 (BMP2, n=15, p=9.0E-4), a TGF-β superfamily member, among others (Table 4).

TABLE 4 Ontology analysis of genes associated with rapid OA progressor DNA methylation models. Canonical pathway p-value Genes associated Antigen 7.08E−04 CIITA, HLA-DPA1, HLA-DPB1, presentation PSMB8, PSMB9, TAP2 AMPK 1.05E−03 AK8, CFTR, CHRM2, CHRNA2, signaling CHRNA9, EEF2, FOXG1, INS, PDPK1, PPM1E, PRKACB, RAB7A, RPTOR, SMARCA4, SMARCD3 Sonic 9.33E−03 GLIS1, GLIS2, PRKACB, SUFU hedgehog signaling Synaptogenesis 1.58E−02 AP2A2, CACNB4, CDH22, CDH23, Signaling CDH4, EIF4EBP3, EPHA8, EPHB3, Pathway FGR, GRIN2B, PRKACB, SHC2, STX1B, SYN2, SYT15, SYT5 Aryl 1.95E−02 ALDH1A3, ARNT, CDK6, CDKN2A, Hydrocarbon NCOA2, NR2F1, RXRG, SMARCA4, Receptor TP73 Signaling Endocannabinoid 2.75E−02 CACNB4, CACNG3, CACNG8, CNR2, Neuronal GNG7, GRIN2B, PRKACB, PTGS2 Synapse Pathway Autophagy 2.82E−02 ATG7, CTSO, LAMP1, SQSTM1, WIPI1 Upstream Molecule Number of regulator type p-value associated genes PITX2 transcription 1.34E−05 14 regulator Bvht long noncoding 5.48E−05 10 RNA histone H3 group 6.93E−05 29 histone H4 group 9.63E−05 14 miR-141 microRNA 1.91E−04 9 ASCL1 transcription 3.09E−04 10 regulator miR-9 microRNA 3.37E−04 5 LHX6 transcription 4.42E−04 5 regulator miR-137 microRNA 8.23E−04 2 BMP2 growth factor 8.96E−04 15

Biomarkers hold great potential for improving clinical outcomes in common chronic diseases including OA. The early identification of OA patients who are likely to progress radiographically, clinically, or both, will allow for the enrichment of clinical trials of disease-modifying antiosteoarthritic drugs (DMOADs) with appropriate patients. Biomarkers of progression may also allow clinicians to stratify early OA patients, offering personalized care by taking into account an individual's likelihood to respond to a particular therapy. In this pilot study, the inventors sought to test whether baseline peripheral blood mononuclear cell DNA methylation data could be used to develop models to discriminate those patients who would go on to experience radiographic progression from nonprogressors. While based on a relatively small number of patients from a single cohort, these results nonetheless suggest that peripheral blood-based epigenetic models may be useful for OA subtype discrimination and should be evaluated in future larger studies of heterogeneous OA patients from additional cohorts.

Several groups have previously investigated biomarkers predictive of future OA progression. The largest biochemical study in this regard was the OAI biomarker studies including the osteoarthritis biomarker consortium of the Foundation for the National Institutes of Health (OABC-FNIH) which investigated a targeted set of biochemical biomarkers as predictors of OA pain and radiographic progression. Their analysis identified a combination of three biochemical biomarkers for discrimination of pain and radiographic progression from nonprogressors with a c-statistic of 0.631[9], although they used a time-integrated concentration (TIC) approach, requiring multiple biomarker measurements over time as input into their prognostic model. This same study also evaluated the predictive capability of baseline biomarkers alone, but these not demonstrate robust differentiation of progressors (c=0.586)[9].

Radiographic biomarkers predicting future disease progression have also been evaluated. In 2016, Collins et al. reported models based on changes in MRI semi-quantitative markers over 24 months to predict the likelihood of radiographic progression at 48 months as part of the OABC-FNIH study[26]; the best model achieved a c-statistic of 0.74. Like the OABC-FNIH biochemical biomarker study, this study leveraged changes in imaging parameters over time to predict future progression. Trabecular bone texture (TBT) is perhaps the best-studied single imaging biomarker for prediction of future OA progression. Kraus et al evaluated this in FNIH patients, with a best composite model using baseline TBT to predict future radiographic progression with a c-statistic of 0.624[27]. This is somewhat lower than previous reports using TBT, Janvier and colleagues, for example, reported a c-statistic of AUC 0.77 in 2017[28].

There have also been recent reports using machine learning to model future progression based on combinations of baseline imaging and demographic data. Joseph and colleagues in 2018 published the results of three such models, with a maximum c-statistic of 0.72 to predict progression to moderate-severe OA over 8 years including demographic data, risk factors, K/L score, cartilage WORMS score, meniscal tear, and cartilage MRI T2 imaging data[29] from the OAI cohort. Also in 2018, Halilaj and colleagues published the results of a mixed-effects mixture model within the OAI cohort to predict joint space narrowing in 1243 subjects. They described an impressive c-statistic of 0.86 for prediction of future progression using a combination of baseline and year 1 follow-up variables, using a 10-cycle, 90% development/10% lockbox validation data splitting approach with 10-fold internal cross-validation, not unlike the methodology of the present invention. Models based solely on baseline data, however, did not predict future radiographic progression (c≤0.6)[30].

Several recent studies have also identified mitochondrial haplotypes as biomarkers which can discriminate OA phenotypes. For example, in 2012 Fernandez-Moreno et al. identified significant increases in cartilage-specific biomarkers of OA in patients carrying mitochondrial haplogroup H associated with the onset of OA [31]. Similarly, this group later identified a decrease in incident OA risk in patients with mitochondrial haplogroup J compared to haplogroup H (HR 0.7, p<0.05) in both the OAI and CHECK cohorts [32], as well as slowing of the rates of radiographic progression rate among OA patients with haplogroup T compared to other haplogroups within the OAI cohort [33]. Future studies should investigate potential complementarity between mitochondrial haplogroups and DNA methylation as predictive OA biomarkers.

Much work has been done over the past several years linking epigenetic changes, particularly DNA methylation, with OA. The present inventors and others have noted differential DNA methylation in inflammatory cell pathways in both cartilage and subchondral bone from OA patients[14-17,34,35]. A subgroup of end-stage OA patients' cartilage demonstrates a fingerprint of epigenetic changes within inflammatory genes[18,36]. Given chondrocyte and subchondral bone DNA methylation aberrancy in both knee and hip OA, along with the known contributions of chronic inflammation and inflammatory gene epigenetic changes to OA, the DNA methylation patterns within PBMCs associated with OA progression the inventors describe in this report are intuitively consistent with previously published data.

The PBMC DNA methylation-based approach taught herein has several advantages over previously published biomarkers. Most notably, this approach offers predictive capability based on a single baseline blood draw. Further, this model demonstrated higher c-statistic values than previously described biochemical biomarkers. A traditional DNA methylation analysis of progressors and nonprogressors was performed and did not identify significantly differentially methylated positions (DMPs) with a false data rate-corrected p-value ≤0.05. This is not particularly surprising given the mixed PBMC population. This approach utilized the combined effects of multiple CpG sites when developing DNA methylation-based predictive models.

Gene ontology analysis revealed several canonical gene pathways and upstream regulators. Unfortunately, there have not been previous epigenetic analyses of peripheral blood cells in OA in humans or mice to compare these data to. However, many pathways and regulators previously described in articular tissues overlap with these findings. For example, AMP kinase (AMPK) deficiency in chondrocytes accelerates both age- and trauma-associated OA in mice[44], whereas a pharmacological stimulator of AMPK attenuates post-traumatic OA in rats[45]. The endocannabinoid system within synovial tissue has been associated with OA pain [46]. Autophagy has been widely associated with OA. Age-related loss of autophagy has been linked with OA severity in human [47] and murine [48] joint tissue. Furthermore, cartilage-specific deletion of mammalian target of rapamycin (mTOR) increases autophagy signaling and protects against post-traumatic OA induction in mice [49]. Among the upstream regulators identified in this ontology analysis was PITX2, a component of the Wnt signaling pathway key to mesenchymal stem cell function which is altered in OA patients [50]. MicroRNA-141 is dysregulated in human OA and contributes to pathogenesis by augmentation of lipid metabolism [51], and is important in maintaining the appropriate expression of key osteoblast differentiation proteins including Runx2, Sclerostin, ALP, and Dlx5[52]. MicroRNA-9 has been shown to directly augment the expression of the key catabolic enzyme matrix metalloproteinase-13 (MMP13) in OA patients [53] and animal models[54]. MicroRNA-137 regulates chondrocyte metabolism via targeting Runx2[55]. Finally, bone morphogenic protein-2 (BMP2) upregulation has been linked to OA development and increased matrix turnover [56]. It is a key regulator of chondrocyte metabolism [57] and has been suggested as a novel OA therapeutic[58].

A major concern with machine learning is generally the problem of overfitting. The inventors reduced this possibility through extensive cross-validation and report the accuracy of models when tested on data unseen during model development. The inventors included in the analysis data from both Illumina 450k and 850k chips. All data from 850k chips were subset to only those sites included on the 450k array and were batch corrected. The inventors saw no evidence for differences in predictive capability with the two chip types (see above). The inventors did see differences comparing M value-based to beta value-based models; however, this is not unsurprising given previous reports of variations in statistical measures of these values [24] owing to differences in scedasticity. There is an emerging literature in the OA field which has demonstrated the importance of activated macrophages in disease development and progression [63-65]. It is important to highlight that the gene ontology analyses performed herein were based on CpG sites selected following PBMC cell composition correction. Thus, the present invention can be used to perform predictive and/or prognostic biomarker analysis, which can include DNA from mixed PBMCs and/or whole blood.

These results demonstrate for the first time the use of peripheral blood epigenetic patterns as predictive models for knee OA radiographic progression. The use of linear modeling applied to a large genome-wide DNA methylation dataset from well-matched case and control cohorts offer the first glimpse into the potential of future OA epigenetic classification. The present invention offers significant advantages over traditional biochemical biomarkers, including requiring a single baseline blood sample. Thus, the present invention provides an easily accessible predictive biomarkers to personalize and improve the care of adults with knee OA.

Study Design. This nested case-control study (116 total patients, 58 progressors, 58 nonprogressors) used data and biospecimens from the Osteoarthritis Initiative (OAI) database, which is available for public access at https://data-archive.nimh.nih.gov/oai/. All Osteoarthritis Initiative (OAI) participants provided written informed consent, and the study was carried out in accordance with the OAI data user agreement, approved by the Committee on Human Research of the Institutional Review Board (IRB) for the University of California, San Francisco (UCSF).

The IRBs of the University of Oklahoma Health Sciences Center and Oklahoma Medical Research Foundation also reviewed and approved the project. Detailed case and control criteria are presented herein below. Participants had baseline and yearly follow-up knee radiographs and PBMC DNA available. Kellgren-Lawrence Grade (KLG) and quantitative joint space width (JSW) [59] were assessed by the central reading site using non-fluoroscopic fixed-flexion knee radiographs with a Synaflexer positioning device (Synaflexor, Synarc, Newark, Calif.). All participants had baseline KLG of 2-3 in at least one knee without a history of total knee joint replacement through 48-months. Participants with a tibial plateau rim distance of 6.5 mm at baseline, or with a change in the rim distance of >2.0 mm between baseline and follow-up were excluded due to unreliable radiographic positioning.

Definition of radiographic progression, case and control group characteristics. The definition of radiographic progression was similar to the case definitions of the OABC-FNIH[9]. Cases had radiographic progression in the medial tibiofemoral compartment by a longitudinal loss in the minimum JSW of at least 0.7 mm from baseline to 24-month follow-up in one index knee, with persistent narrowing in the same index knee at 48 months based on radiographs obtained from a non-fluoroscopic fixed flexion protocol (Synaflexor, Synarc, Newark, Calif.). In each case, the contralateral (non-index) knee had less progression than the index knee, or no progression over the follow-up period. Participants with a tibial plateau rim distance of 6.5 mm at baseline, or with a change in the rim distance of >2.0 mm between baseline and follow-up were excluded due to inappropriate and/or unreliable radiographic positioning. Non-progressors were defined as those with ≤0.5 mm of JSW loss from baseline to 48 months in either knee. These thresholds were set to coincide with previous OAI biomarker studies[9,60,62,66], as defined in the Foundation for the National Institutes of Health biomarker consortium project (OABC-FNIH) and were set based on the distribution of 1-month change in minimum JSW in normal knees of OAI control participants and estimated to have ≤10% probability of change due to measurement error[8,67].

Controls were frequency matched with cases by age category, sex, race, and BMI category as shown in Table 1 and were also frequency matched with the larger OAI cohort to broaden the applicability of these findings. Group differences were calculated using a Student t-test and statistically analyzed using a 2-tailed P value. There were no differences among the two groups in any demographic category with the exception of mean baseline Western Ontario and McMaster (WOMAC) pain subscale (Table 1), although it should be noted that there was a trend towards fewer females included among cases (53% vs. 60%, p=0.13), more NSAID use at baseline among cases (29% vs. 17%, p=0.13), and an increased mean baseline K/L grade among cases (2.2 vs. 2.0, p=0.09), although no difference in mean baseline JSW was noted in cases (3.9 vs. 4.0, p=0.34). The inventors also evaluated the presence of various comorbid conditions among data collected by the OAI, including history of heart attack, failure, stroke, pulmonary disease, diabetes, and cancer (Table 1). The inventors adjusted these models for these variables as part of the analysis (see below).

DNA methylation assays, PBMC composition assessment and adjustment. Five hundred nanograms of DNA was treated with sodium bisulfite (EZ DNA methylation kit, Zymo) and loaded onto Illumina Infinium HumanMethylation450k (n=62 samples: 30 cases, 32 controls) or 850k (n=54 samples: 28 cases, 26 controls) arrays. As no direct measures of PBMC cell type composition were available from the OAI, these data were estimated using the estimate Cell Counts function of minfi. No statistically significant differences in estimated PBMC cell composition were found between groups (Table 1, Table 5), although there was a trend towards increased monocytes among cases (7.4±0.3% vs. 6.7±0.3%, cases vs. controls mean±SEM, p=0.12). DNA methylation data were corrected for cell count variation using frozen surrogate variable analysis [22] via the sva package (v. 3.28.0). This method has been previously shown to robustly correct for cell count variation and other batch effects in large-scale epigenomic studies [22,23,68].

TABLE 5 UCSC_(—) RELATION_(—) Beta M GENOME_(—) UCSC_REFGENE_(—) UCSC_REFGENE_(—) REFGENE_(—) UCSC_CPG_(—) TO_UCSC_(—) TargetID counts counts BUILD CHR MAPINFO NAME ACCESSION GROUP ISLANDS_NAME CPG_ISLAND cg00002464 1 37 8 120428418 NOV NM_002514 TSS200 chr8: 120428398-120429178 Island cg00027745 2 37 7 1452678 chr7: 1452417-1452794 Island cg00089154 1 37 16 57352732 cg00105102 2 37 1 156217178 PAQR6; PAQR6 NM_024897; NM_198406 5′UTR; 5′UTR chr1: 156215368-156215899 S_Shore cg00105102 2 37 1 156217178 PAQR6; PAQR6 NM_024897; NM_198406 5′UTR; 5′UTR chr1: 156215368-156215899 S_Shore cg00107890 1 37 15 71492746 THSD4 NM_024817 Body cg00125544 1 37 2 236865931 AGAP1; AGAP1 NM_014914; NM_001037131 Body; Body chr2: 236867652-236867906 N_Shore cg00142933 1 37 2 128420784 LIMS2; LIMS2; NM_001136037; NM_017980; Body; Body; chr2: 128421719-128422182 N_Shore LIMS2; LIMS2 NM_001161403; NM_001161404 Body; 5′UTR cg00142933 8 37 2 128420784 LIMS2; LIMS2; NM_001136037; NM_017980; Body; Body; chr2: 128421719-128422182 N_Shore LIMS2; LIMS2 NM_001161403; NM_001161404 Body; 5′UTR cg00143249 5 37 7 156798810 MNX1; MNX1 NM_001165255; NM_005515 Body; Body chr7: 156795355-156799394 Island cg00143249 1 37 7 156798810 MNX1; MNX1 NM_001165255; NM_005515 Body; Body chr7: 156795355-156799394 Island cg00152637 1 37 6 28104690 chr6: 28104781-28105240 N_Shore cg00180559 1 37 1 233496768 KIAA1804 NM_032435 Body chr1: 233497707-233497917 N_Shore cg00192026 1 37 4 174411279 cg00278028 3 37 22 28196834 MN1; MN1 NM_002430; NM_002430 5′UTR; 1stExon chr22: 28192793-28198592 Island cg00290605 1 37 22 32366707 chr22: 32366492-32367061 Island cg00308618 1 37 2 152831903 CACNB4; CACNB4; NM_000726; NM_001145798; Body; Body; CACNB4; CACNB4 NM_001005747; NM_001005746 TSS1500; Body cg00335286 2 37 18 13916355 MC2R NM_000529 TSS1500 cg00336071 1 37 15 63449943 RPS27L NM_015920 TSS1500 chr15: 63449418-63449874 S_Shore cg00355514 1 37 13 24914782 chr13: 24914548-24915100 Island cg00386663 1 37 16 692659 FAM195A NM_138418 Body chr16: 691597-692700 Island cg00388154 1 37 15 68498857 CALML4; CALML4 NM_001031733; NM_033429 TSS1500; TSS1500 cg00401433 1 37 8 106674239 ZFPM2 NM_012082 Body cg00409636 1 37 2 75720541 FAM176A; FAM176A NM_001135032; NM_032181 Body; Body cg00466544 1 37 14 57046243 C14orf101 NM_017799 TSS1500 chr14: 57046472-57046804 N_Shore cg00491335 1 37 2 224705654 chr2: 224701962-224702790 S_Shelf cg00496805 1 37 19 57901154 ZNF548 NM_152909 TSS200 chr19: 57901091-57901517 Island cg00497251 1 37 2 241508725 RNPEPL1 NM_018226 5′UTR chr2: 241507463-241507669 S_Shore cg00510552 2 37 16 4511987 NMRAL1 NM_020677 Body cg00551143 1 37 7 28998860 TRIL NM_014817 TSS1500 chr7: 28995305-28998541 S_Shore cg00562641 1 37 5 68789255 OCLN NM_002538 5′UTR chr5: 68788151-68789823 Island cg00572243 1 37 8 28458806 cg00587472 1 37 2 6952860 cg00607154 1 37 5 6754116 POLS NM_006999 Body chr5: 6755104-6755387 N_Shore cg00618507 1 37 7 102096322 ORAI2; ORAI2 NM_032831; NM_001126340 3′UTR; 3′UTR chr7: 102097927-102098384 N_Shore cg00704844 1 37 6 32821621 PSMB9; TAP1; NM_002800; NM_000593; TSS1500; 5′UTR; chr6: 32820849-32822370 Island PSMB9; TAP1 NM_148954; NM_000593 TSS1500; 1stExon cg00704844 1 37 6 32821621 PSMB9; TAP1; NM_002800; NM_000593; TSS1500; 5′UTR; chr6: 32820849-32822370 Island PSMB9; TAP1 NM_148954; NM_000593 TSS1500; 1stExon cg00708678 1 37 10 91294839 SLC16A12 NM_213606 5′UTR chr10: 91294947-91295925 N_Shore cg00712762 2 37 1 36351470 EIF2C1 NM_012199 Body chr1: 36348501-36349731 S_Shore cg00796164 1 37 19 57654968 ZIM3 NM_052882 5′UTR cg00819788 1 37 17 7308579 C17orf61 NM_152766 TSS1500 chr17: 7307206-7308626 Island cg00859178 1 37 1 162467208 UHMK1 NM_175866 TSS1500 chr1: 162467599-162468027 N_Shore cg00878038 1 37 7 151107807 WDR86 NM_198285 TSS1500 chr7: 151106244-151107808 Island cg00886571 1 37 14 105293199 chr14: 105293183-105293395 Island cg00891611 1 37 1 108066602 cg00943060 1 37 7 65211784 chr7: 65215732-65216495 N_Shelf cg00989986 1 37 8 49746558 chr8: 49747395-49747621 N_Shore cg01022859 1 37 17 60767314 MRC2 NM_006039 Body cg01029669 1 37 19 46999840 PNMAL2 NM_020709 TSS1500 chr19: 46996327-46998437 S_Shore cg01062913 1 37 1 149169973 cg01090026 2 37 6 39692382 KIF6 NM_145027 Body chr6: 39692743-39692966 N_Shore cg01110552 1 37 10 103578627 MGEA5; MGEA5 NM_001142434; NM_012215 TSS1500; TSS1500 chr10: 103577394-103578256 S_Shore cg01120851 1 37 1 6657644 KLHL21 NM_014851 Body chr1: 6659125-6659505 N_Shore cg01125463 1 37 6 42946178 PEX6 NM_000287 1stExon chr6: 42946310-42947127 N_Shore cg01138671 1 37 6 32130686 PPT2; PPT2 NM_005155; NM_138717 Body; Body chr6: 32134460-32135196 N_Shelf cg01144965 1 37 8 1811760 ARHGEF10 NM_014629 Body cg01166564 1 37 2 26987492 C2orf18 NM_017877 Body chr2: 26987030-26987500 Island cg01198033 1 37 7 155302342 CNPY1 NM_001103176 5′UTR chr7: 155302253-155303158 Island cg01232267 1 37 3 47398209 chr3: 47397811-47398210 Island cg01263999 1 37 13 108435129 FAM155A NM_001080396 Body cg01309395 1 37 6 33091795 HLA-DPB2 NR_001435 Body cg01316857 2 37 19 48685724 chr19: 48685723-48686085 Island cg01333080 1 37 3 183994568 ECE2; ECE2; NM_001100120; NM_001037324; Body; Body; chr3: 183993905-183994347 S_Shore ECE2; ECE2 NM_014693; NM_001100121 Body; Body cg01338043 1 37 7 100136013 AGFG2 NM_006076 TSS1500 chr7: 100136448-100136919 N_Shore cg01392841 1 37 19 47016869 chr19: 47016848-47017118 Island cg01427750 1 37 12 131529339 GPR133 NM_198827 Body chr12: 131529297-131529887 Island cg01514015 1 37 1 236318427 GPR137B NM_003272 Body cg01515114 1 37 4 4139730 cg01543583 1 37 14 59947673 C14orf149 NM_144581 Body chr14: 59950460-59951527 N_Shelf cg01548562 1 37 9 71836408 TJP2; TJP2; NM_001170414; NM_001170630; Body; Body; chr9: 71835913-71836409 TJP2; TJP2; NM_001170415; NM_201629; Body; Body; TJP2; TJP2 NM_004817; NM_001170416 Body; Body cg01565438 2 37 17 33776554 SLFN13 NM_144682 TSS1500 chr17: 33776553-33776888 Island cg01591416 1 37 8 30601572 UBXN8 NM_005671 TSS200 cg01620570 1 37 17 15165908 PMP22; PMP22 NM_153321; NM_000304 TSS200; 5′UTR chr17: 15165796-15166506 Island cg01709473 1 37 6 12010960 chr6: 12012543-12013379 N_Shore cg01709473 1 37 6 12010960 chr6: 12012543-12013379 N_Shore cg01721429 1 37 16 47007486 DNAJA2; DNAJA2 NM_005880; NM_005880 5′UTR; 1stExon chr16: 47006827-47008029 Island cg01771479 1 37 8 144198810 cg01867419 1 37 6 30421515 chr6: 30418844-30419630 S_Shore cg01872216 1 37 14 54430382 chr14: 54430154-54430670 Island cg01900413 1 37 11 128419356 ETS1 NM_001143820 Body chr11: 128419198-128419513 Island cg01962086 1 37 3 195637027 TNK2 NM_005781 TSS1500 chr3: 195635359-195636895 S_Shore cg02055540 1 37 5 165510804 cg02071447 1 37 5 151304542 GLRA1; GLRA1 NM_000171; NM_001146040 TSS200; TSS200 chr5: 151304226-151304824 Island cg02148547 1 37 14 21457502 METT11D1; METT11D1 NM_001029991; NM_022734 TSS1500; TSS1500 chr14: 21458389-21458608 N_Shore cg02192318 1 37 16 89500212 ANKRD11 NM_013275 5′UTR chr16: 89500025-89500226 Island cg02205746 1 37 16 2732724 KCTD5 NM_018992 1stExon chr16: 2732272-2732940 Island cg02215141 2 37 4 132663979 chr4: 132664263-132664658 N_Shore cg02215141 6 37 4 132663979 chr4: 132664263-132664658 N_Shore cg02216246 2 37 11 128564756 FLI1; FLI1 NM_002017; NM_001167681 Body; 5′UTR chr11: 128562671-128565011 Island cg02216246 1 37 11 128564756 FLI1; FLI1 NM_002017; NM_001167681 Body; 5′UTR chr11: 128562671-128565011 Island cg02241363 2 37 17 78450357 NPTX1; NPTX1 NM_002522; NM_002522 5′UTR; 1stExon chr17: 78449507-78452783 Island cg02268171 2 37 13 24477610 chr13: 24477426-24478053 Island cg02275394 1 37 13 80917432 chr13: 80914013-80915574 S_Shore cg02275622 1 37 2 207773017 cg02286547 2 37 11 75920278 chr11: 75918741-75922084 Island cg02301193 1 37 1 90267201 cg02301193 1 37 1 90267201 cg02309335 1 37 6 30227294 HLA-L NR_027822 TSS200 chr6: 30227320-30228255 N_Shore cg02339418 1 37 12 123717776 C12orf65; C12orf65 NM_152269; NM_001143905 TSS200; TSS1500 chr12: 123717367-123718388 Island cg02358630 1 37 10 71993457 PPA1 NM_021129 TSS1500 chr10: 71992414-71993467 Island cg02368096 2 37 7 98248993 NPTX2 NM_002523 Body chr7: 98245805-98247759 S_Shore cg02398007 2 37 12 67616546 cg02398007 1 37 12 67616546 cg02444810 1 37 17 27055702 NEK8 NM_178170 TSS200 chr17: 27055187-27056056 Island cg02448190 2 37 1 156030535 RAB25 NM_020387 TSS1500 cg02448190 1 37 1 156030535 RAB25 NM_020387 TSS1500 cg02491138 1 37 20 51589616 TSHZ2; TSHZ2 NM_173485; NM_173485 1stExon; 5′UTR chr20: 51589707-51590020 N_Shore cg02503646 1 37 3 52444059 PHF7; PHF7; NM_173341; NM_016483; TSS1500; TSS1500; chr3: 52443677-52445104 Island BAP1 NM_004656 TSS200 cg02504716 1 37 11 124071642 cg02529035 1 37 2 220377885 ACCN4; ACCN4 NM_182847; NM_018674 TSS1500; TSS1500 chr2: 220377743-220377946 Island cg02554361 1 37 16 11001757 CIITA NM_000246 Body chr16: 11001646-11001872 Island cg02558537 1 37 11 107328586 CWF19L2 NM_152434 TSS200 chr11: 107328441-107328691 Island cg02574502 1 37 19 54486058 CACNG8 NM_031895 Body chr19: 54485303-54486322 Island cg02625590 1 37 19 41880276 TMEM91 NM_001098825 5′UTR chr19: 41882507-41882773 N_Shelf cg02633148 1 37 4 46391476 GABRA2; GABRA2 NM_001114175; NM_000807 TSS200; 5′UTR chr4: 46391903-46392572 N_Shore cg02653364 1 37 16 58283706 CCDC113; CCDC113 NM_001142302; NM_014157 TSS200; TSS200 chr16: 58283703-58284084 Island cg02704217 1 37 17 12568507 MYOCD; MYOCD NM_153604; NM_001146312 TSS1500; TSS1500 chr17: 12568667-12569335 N_Shore cg02721947 1 37 5 39719620 chr5: 39721548-39721835 N_Shore cg02734521 1 37 6 108326291 cg02804100 1 37 19 720993 PALM; PALM NM_002579; NM_001040134 Body; Body chr19: 719098-720953 S_Shore cg02811702 1 37 13 24901961 chr13: 24902292-24902696 N_Shore cg02846648 1 37 12 129416689 GLT1D1 NM_144669 Body cg02862362 1 37 6 131895102 ARG1 NM_000045 Body cg02894027 1 37 2 17375162 cg02904235 1 37 14 91527369 RPS6KA5; RPS6KA5 NM_182398; NM_004755 TSS1500; TSS1500 chr14: 91526233-91527552 Island cg02947232 1 37 20 42937544 FITM2 NM_001080472 Body chr20: 42939 450-42940043 N_Shore cg02962630 5 37 15 41222776 DLL4 NM_019074 Body chr15: 41217789-41223180 Island cg02962630 4 37 15 41222776 DLL4 NM_019074 Body chr15: 41217789-41223180 Island cg02991338 1 37 14 29236017 FOXG1 NM_005249 TSS1500 chr14: 29236835-29237832 N_Shore cg03003722 2 37 6 38035488 ZFAND3 NM_021943 Body cg03004273 1 37 18 7568265 PTPRM; PTPRM NM_002845; NM_001105244 Body; Body chr18: 7566557-7568830 Island cg03054162 1 37 2 70485230 PCYOX1; PCYOX1 NM_016297; NM_016297 1stExon; 5′UTR chr2: 70485231-70485679 N_Shore cg03069383 1 37 2 18741691 RDH14 NM_020905 1stExon chr2: 18741356-18741964 Island cg03069736 1 37 17 72542117 CD300C; CD300C NM_006678; NM_006678 1stExon; 5′UTR cg03088705 1 37 10 111624928 XPNPEP1; XPNPEP1; NR_030724; NM_001167604; Body; 3′UTR; XPNPEP1 NM_020383 3′UTR cg03103023 1 37 1 25088406 CLIC4 NM_013943 Body cg03119288 1 37 19 10829265 DNM2; DNM2; NM_004945; NM_001005361; Body; Body; chr19: 10828657-10829340 Island DNM2; DNM2 NM_001005362; NM_001005360 Body; Body cg03124231 1 37 4 174255570 HMGB2; HMGB2; NM_001130689; NM_002129; TSS1500; 1stExon; chr4: 174254683-174256538 Island HMGB2; HMGB2 NM_001130688; NM_002129 TSS200; 5′UTR cg03212634 4 37 19 54292238 cg03212634 9 37 19 54292238 cg03243450 1 37 5 1800782 NDUFS6; MRPL36 NM_004553; NM_032479 TSS1500; TSS1500 chr5: 1799461-1801905 Island cg03243450 5 37 5 1800782 NDUFS6; MRPL36 NM_004553; NM_032479 TSS1500; TSS1500 chr5: 1799461-1801905 Island cg03249986 1 37 11 66383717 RBM14 NM_006328 TSS1500 chr11: 66383571-66385047 Island cg03290040 1 37 22 24110355 CHCHD10 NM_213720 TSS1500 chr22: 24110029-24110995 Island cg03290752 1 37 3 176915082 TBL1XR1 NM_024665 TSS200 chr3: 176915511-176915854 N_Shore cg03318904 1 37 22 39801522 MAP3K7IP1; MAP3K7IP1 NM_006116; NM_153497 Body; Body cg03331282 1 37 1 36056567 TFAP2E NM_178548 Body cg03382797 1 37 9 135755363 C9orf98; C9orf9 NM_152572; NM_018956 TSS1500; 5′UTR chr9: 135753347-135754384 S_Shore cg03396103 1 37 12 116946354 chr12: 116946195-116946607 Island cg03396325 1 37 15 87876345 cg03414134 2 37 3 187462086 BCL6 NM_001706 5′UTR chr3: 187461974-187462197 Island cg03440588 3 37 1 47900320 FOXD2; MGC12982 NM_004474; NR026878 TSS1500; TSS200 chr1: 47899661-47900385 Island cg03440588 3 37 1 47900320 FOXD2; MGC12982 NM_004474; NR026878 TSS1500; TSS200 chr1: 47899661-47900385 Island cg03448396 1 37 3 38495949 LOC100128640; ACVR2B NR_028389; NM_001106 Body; Body chr3: 38495088-38497151 Island cg03539051 1 37 19 56418660 NLRP13 NM_176810 Body cg03558399 2 37 3 67022555 cg03558805 1 37 7 73184883 CLDN3 NM_001306 TSS1500 chr7: 73183379-73185115 Island cg03586240 1 37 7 1966361 MAD111; MAD111; NM_003550; NM_001013837; Body; Body; chr7: 1967664-1967994 N_Shore MAD111 NM_001013836 Body cg03593908 1 37 13 60842299 cg03597540 1 37 1 149857491 HIST2H2BE; HIST2H2AC; NM_003528; NM_003517; 1stExon; TSS1500; chr1: 149857769-149859470 N_Shore HIST2H2BE NM_003528 3′UTR cg03623968 1 37 3 128523333 RAB7A NM_004637 Body cg03632289 1 37 11 71301062 cg03657549 2 37 7 128116813 METTL2B; METTL2B NM_018396; NM_018396 5′UTR; 1stExon chr7: 128116667-128117312 Island cg03672997 1 37 10 7859623 TAF3 NM_031923 TSS1500 chr10: 7860261-7861107 N_Shore cg03677929 1 37 12 7342174 PEX5; PEX5; NM_000319; NM_001131023; TSS1500; TSS200; chr12: 7342074-7342417 Island PEX5; PEX5; PEX5 NM_001131025; NM_001131024; TSS200; TSS200; NM_001131026 5′UTR cg03677929 1 37 12 7342174 PEX5; PEX5; NM_000319; NM_001131023; TSS1500; TSS200; chr12: 7342074-7342417 Island PEX5; PEX5; PEX5 NM_001131025; NM_001131024; TSS200; TSS200; NM_001131026 5′UTR cg03687650 7 37 11 3144685 OSBPL5; OSBPL5; NM_020896; NM_001144063; Body; Body; chr11: 3141642-3141877 S_Shelf OSBPL5 NM_145638 Body cg03687650 11 37 11 3144685 OSBPL5; OSBPL5; NM_020896; NM_001144063; Body; Body; chr11: 3141642-3141877 S_Shelf OSBPL5 NM_145638 Body cg03703325 1 37 3 50606864 HEMK1 NM_016173 TSS200 chr3: 50606345-50606972 Island cg03733229 2 37 21 46824701 COL18A1 NM_130445 TSS1500 chr21: 46824531-46826234 Island cg03799405 2 37 4 1595726 chr4: 1595293-1595539 S_Shore cg03822003 1 37 16 30569878 ZNF764 NM_033410 TSS1500 chr16: 30569181-30570049 Island cg03870777 10 37 12 53342755 KRT18; KRT18 NM_000224; NM_199187 TSS200; 5′UTR chr12: 53342805-53343162 N_Shore cg03870777 6 37 12 53342755 KRT18; KRT18 NM_000224; NM_199187 TSS200; 5′UTR chr12: 53342805-53343162 N_Shore cg03916104 1 37 1 6314748 GPR153 NM_207370 Body chr1: 6313761-6314139 S_Shore cg03928690 1 37 2 198381209 MOBKL3; MOBKL3; NM_199482; NM_001100819; 5′UTR; Body; chr2: 198380423-198381301 Island MOBKL3 NM_015387 Body cg03937591 1 37 4 899553 GAK NM_005255 Body chr4: 899774-899985 N_Shore cg04016326 1 37 12 14132940 GRIN2B; GRIN2B NM_000834; NM_000834 1stExon; 5′UTR chr12: 14134626-14135242 N_Shore cg04035728 1 37 8 27323467 CHRNA2 NM_000742 Body chr8: 27320914-27321276 S_Shelf cg04072156 1 37 3 148544962 CPB1 NM_001871 TSS1500 cg04083921 2 37 5 130915922 RAPGEF6; RAPGEF6; NM_001164388; NM_001164386; Body; Body; RAPGEF6; RAPGEF6; NM_001164390; NM_001164389; Body; Body; RAPGEF6; RAPGEF6 NM_001164387; NM_016340 Body; Body cg04101351 1 37 12 20522672 PDE3A NM_000921 1stExon chr12: 20521616-20523122 Island cg04113418 1 37 19 49646093 PPFIA3 NM_003660 Body chr19: 49646092-49646308 Island cg04120546 1 37 8 125740895 MTSS1 NM_014751 TSS200 chr8: 125739685-125741266 Island cg04166812 1 37 14 61122051 chr14: 61123613-61124613 N_Shore cg04171803 1 37 2 233561907 GIGYF2; GIGYF2; NM_015575; NM_001103148; TSS200; TSS200; chr2: 233562005-233562547 N_Shore GIGYF2; GIGYF2 NM_001103146; NM_001103147 TSS200; TSS200 cg04186622 1 37 1 148556562 chr1: 148555640-148556626 Island cg04199621 1 37 6 30955712 MUC21 NM_001010909 Body cg04215672 1 37 4 4108791 chr4: 4108734-4109499 Island cg04223160 1 37 14 23755398 HOMEZ NM_020834 TSS200 chr14: 23755121-23755456 Island cg04254690 1 37 4 25031951 LGI2 NM_018176 Body chr4: 25032028-25032311 N_Shore cg04262428 2 37 11 70673256 SHANK2 NM_012309 Body chr11: 70672834-70673055 S_Shore cg04285141 2 37 16 57872427 cg04285141 1 37 16 57872427 cg04293489 1 37 6 49917881 DEFB133 NM_001166478 TSS1500 cg04357082 1 37 16 980022 LMF1 NM_022773 Body chr16: 979785-980198 Island cg04357082 1 37 16 980022 LMF1 NM_022773 Body chr16: 979785-980198 Island cg04360049 1 37 1 158150797 CD1D NM_001766 5′UTR chr1: 158150620-158151503 Island cg04381865 1 37 16 15219673 chr16: 15221568-15222202 N_Shore cg04406981 1 37 19 48453315 SNAR-C3 NR_024221 TSS1500 cg04427003 4 37 5 63257499 HTR1A NM_000524 1stExon chr5: 63256548-63257886 Island cg04441477 4 37 16 24267399 CACNG3; CACNG3 NM_006539; NM_006539 1stExon; 5′UTR chr16: 24267040-24267527 Island cg04493430 1 37 16 1030388 SOX8 NM_014587 TSS1500 chr16: 1029878-1035327 Island cg04498153 1 37 7 157690139 PTPRN2; PTPRN2; NM_002847; NM_130842; Body; Body; chr7: 157690559-157690770 N_Shore PTPRN2 NM_130843 Body cg04498153 3 37 7 157690139 PTPRN2; PTPRN2; NM_002847; NM_130842; Body; Body; chr7: 157690559-157690770 N_Shore PTPRN2 NM_130843 Body cg04529860 2 37 19 39900650 chr19: 39900139-39900888 Island cg04544058 1 37 3 13609195 FBLN2; FBLN2; NM_001165035; NM_001004019; TSS1500; 5′UTR; chr3: 13611923-13612435 N_Shelf FBLN2 NM_001998 5′UTR cg04574459 1 37 21 47010768 chr21: 47009996-47011163 Island cg04691540 1 37 1 179198414 ABL2; ABL2; ABL2; NM_001136001; NM_001168238; 1stExon; 1stExon; chr1: 179198163-179199200 Island ABL2; ABL2 NM_001168236; NM_007314; 1stExon; 1stExon; NM_001168237 1stExon cg04706600 2 37 5 178741004 ADAMTS2; ADAMTS2 NM_021599; NM_014244 Body; Body cg04706600 4 37 5 178741004 ADAMTS2; ADAMTS2 NM_021599; NM_014244 Body; Body cg04723723 1 37 1 67966270 cg04729004 1 37 7 128550932 KCP; KCP NM_001135914; NM_199349 TSS200; TSS200 chr7: 128550409-128550903 S_Shore cg04737185 1 37 11 1445041 BRSK2 NM_003957 Body cg04786330 1 37 12 27091356 C12orf11; FGFR1OP2; NM_018164; NM_015633; TSS200; 5′UTR; chr12: 27091158-27091857 Island FGFR1OP2 NM_015633 1stExon cg04819714 1 37 11 100861375 FLJ32810; TMEM133 NM_152432; NM_032021 3′UTR; TSS1500 cg04821026 1 37 21 15068553 chr21: 15068825-15070104 N_Shore cg04837170 1 37 16 1494876 CCDC154 NM_001143980 TSS1500 chr16: 1495039-1495366 N_Shore cg04884908 2 37 2 72374840 CYP26B1 NM_019885 1stExon chr2: 72371121-72375004 Island cg04891086 1 37 12 5018513 KCNA1 NM_000217 TSS1500 chr12: 5018585-5021171 N_Shore cg04899500 1 37 19 48965791 KCNJ14; KCNJ14 NM_170720; NM_013348 Body; Body chr19: 48965002-48965792 Island cg05025392 1 37 17 14738114 cg05070971 2 37 21 43239518 PRDM15; PRDM15 NM_022115; NM_001040424 Body; Body chr21: 43240351-43240586 N_Shore cg05070971 1 37 21 43239518 PRDM15; PRDM15 NM_022115; NM_001040424 Body; Body chr21: 43240351-43240586 N_Shore cg05088794 1 37 18 33081137 chr18: 33077545-33078063 S_Shelf cg05101846 1 37 17 72580962 C17orf77; CD300LD NM_152460; NM_001115152 TSS200; Body cg05157470 1 37 6 28937310 cg05229450 1 37 6 169465101 cg05240017 2 37 5 40756081 TTC33 NM_012382 TSS200 chr5: 40755537-40756257 Island cg05240017 1 37 5 40756081 TTC33 NM_012382 TSS200 chr5: 40755537-40756257 Island cg05242257 1 37 16 2588092 PDPK1; PDPK1; NM_031268; NM_002613; 5′UTR; 1stExon; chr16: 2588034-2588556 Island PDPK1; PDPK1 NM_031268; NM_002613 1stExon; 5′UTR cg05304037 1 37 19 50094202 PRR12; PRRG2 NM_020719; NM_000951 TSS1500; 3′UTR chr19: 50093657-50095507 Island cg05377387 1 37 16 84328658 WFDC1 NM_021197 1stExon chr16: 84328519-84328720 Island cg05388057 1 37 1 78226545 USP33; USP33; NM_015017; NM_201626; TSS1500; TSS1500; chr1: 78224843-78225650 S_Shore USP33 NM_201624 TSS1500 cg05436007 1 37 6 147213060 cg05436007 1 37 6 147213060 cg05553502 1 37 5 92924091 NR2F1 NM_005654 Body chr5: 92923487-92924497 Island cg05587853 7 37 3 135914748 MSL2; MSL2 NM_001145417; NM_018133 TSS1500; TSS200 chr3: 135914197-135916090 Island cg05592114 1 37 12 7244104 C1R NM_001733 Body cg05597349 1 37 10 102882978 TLX1NB NM_001085398 5′UTR chr10: 102882977-102883551 Island cg05634255 1 37 4 138864033 cg05668926 1 37 7 39609343 C7orf36 NM_020192 Body chr7: 39605776-39606376 S_Shelf cg05743054 2 37 3 158288903 MLF1; MLF1; NM_001130156; NM_022443; TSS200; TSS200; chr3: 158288800-158289271 Island MLF1 NM_001130157 TSS200 cg05757007 1 37 6 101053555 ASCC3 NM_006828 Body cg05835009 1 37 4 710272 PCGF3 NM_006315 5′UTR chr4: 713927-714137 N_Shelf cg05851240 1 37 18 72201663 CNDP1 NM_032649 TSS200 cg05852760 1 37 7 23508224 IGF2BP3 NM_006547 Body chr7: 23508184-23509712 Island cg05854114 1 37 12 77719408 chr12: 77718453-77719440 Island cg05907237 1 37 10 126849609 CTBP2; CTBP2; NM_001083914; NM_001083914; 1stExon; 5′UTR; chr10: 126847224-126851327 Island CTBP2 NM_001329 TSS1500 cg05931119 1 37 6 168569742 cg05936555 2 37 6 30539508 ABCF1; ABCF1 NM_001090; NM_001025091 Body; Body chr6: 30538983-30539487 S_Shore cg05952475 1 37 6 163681845 PACRG; PACRG; NM_152410; NM_001080378; Body; Body; Island PACRG NM_001080379 Body cg05963872 1 37 7 63652631 chr7: 63652630-63652962 cg06016354 3 37 6 32163966 GPSM3; NOTCH4 NM_022107; NM_004557 TSS1500; Body chr6: 32163292-32164383 Island cg06039161 1 37 11 70672835 SHANK2 NM_012309 Body chr11: 70672834-70673055 Island cg06079468 1 10 81839181 LOC219347; LOC219347; NR_027430; NR_027431; TSS1500; TSS1500; chr10: 81838359-81839078 S_Shore LOC219347; C10orf57; NR_027428; NM_025125; TSS1500; Body; LOC219347; LOC219347 NR_027432; NR_027429 TSS1500; TSS1500 cg06081199 1 37 7 117120064 CFTR; CFTR NM_000492; NM_000492 1stExon; 5′UTR cg06087019 1 37 3 27770182 chr3: 27771638-27771942 N_Shore cg06090383 1 37 4 174292579 SAP30 NM_003864 1stExon chr4: 174291879-174293273 Island cg06098215 2 37 10 51575702 NCOA4; NCOA4; NM_005437; NM_001145263; 5′UTR; 5′UTR; chr10: 51572198-51572620 S_Shelf NCOA4; NCOA4; NM_001145261; NM_001145262; Body; TSS1500; NCOA4 NM_001145260 Body cg06153883 1 37 7 136683107 CHRM2; CHRM2; NM_001006631; NM_000739; 5′UTR; 5′UTR; CHRM2; CHRM2; NM_001006627; NM_001006628; 5′UTR; 5′UTR; CHRM2; CHRM2; NM_001006629; NM_001006632; 5′UTR; 5′UTR; CHRM2; CHRM2 NM_001006630; NM_001006626 5′UTR; 5′UTR cg06166932 1 37 8 143530800 chr8: 143530645-143530872 Island cg06180519 2 37 10 32800689 CCDC7; CCDC7 NM_145023; NM_001026383 Body; Body cg06180519 3 37 10 32800689 CCDC7; CCDC7 NM_145023; NM_001026383 Body; Body cg06212297 1 37 16 48079666 cg06254801 2 37 9 79379216 PCA3; PRUNE2 NR_015342; NM_015225 TSS200; Body cg06319785 1 37 2 75437207 cg06326713 1 37 17 20745278 chr17: 20746783-20747635 N_Shore cg06329022 5 37 17 26926511 SPAG5 NM_006461 TSS1500 chr17: 26925742-26926512 Island cg06354519 1 37 1 27939417 FGR; FGR; NM_005248; NM_001042729; 3′UTR; 3′UTR; chr1: 27941865-27942324 N_Shelf FGR NM_001042747 3′UTR cg06409741 11 37 13 114767222 RASA3 NM_007368 Body chr13: 114766710-114767223 Island cg06409741 11 37 13 114767222 RASA3 NM_007368 Body chr13: 114766710-114767223 Island cg06444730 1 37 1 84544284 PRKACB; PRKACB NM_002731; NM_207578 Body; Body chr1: 84543146-84544261 S_Shore cg06452419 1 37 17 55938940 chr17: 55939088-55939591 N_Shore cg06456389 2 37 10 99052468 ARHGAP19 NM_032900 TSS200 chr10: 99051934-99052490 Island cg06466917 1 37 5 17216259 LOC285696; BASP1 NR_027253; NM_006317 Body; TSS1500 chr5: 17216489-17217036 N_Shore cg06483559 1 37 11 123624914 OR6X1 NM_001005188 1stExon cg06502456 2 37 15 25304609 SNORD116-4 NR_003319 TSS200 cg06502456 1 37 15 25304609 SNORD116-4 NR_003319 TSS200 cg06515771 1 37 6 26614168 chr6: 26614013-26614851 Island cg06521472 1 37 16 88990232 CBFA2T3; CBFA2T3 NM_175931; NM_005187 5′UTR; Body chr16: 88994137-88994442 N_Shelf cg06525193 1 37 2 238145456 cg06525491 5 37 11 71353991 chr11: 71350345-71350998 S_Shelf cg06528306 1 37 8 53852661 NPBWR1 NM_005285 1stExon chr8: 53851701-53854426 Island cg06546406 2 37 1 39269756 chr1: 39269729-39270251 Island cg06577604 1 37 3 184279443 EPHB3 NM_004443 TSS200 chr3: 184279194-184280721 Island cg06594186 1 37 7 12971260 cg06638787 1 37 6 5997243 chr6: 5997027-5997414 Island cg06677013 1 37 6 84570388 CYB5R4 NM_016230 Body chr6: 84569263-84569619 S_Shore cg06681324 2 37 2 165000237 cg06681324 1 37 2 165000237 cg06731021 1 37 6 116442866 COL10A1; NT5DC1 NM_000493; NM_152729 Body; Body cg06766273 2 37 11 62521983 ZBTB3 NM_024784 TSS1500 chr11: 62521370-62521962 S_Shore cg06796869 1 37 1 228471009 OBSCN; OBSCN NM_052843; NM_001098623 Body; Body chr1: 228473835-228474043 N_Shelf cg06800849 1 37 16 89180587 ACSF3; ACSF3; NM_174917; NR_023316; Body; Body; ACSF3 NM_001127214 Body cg06816239 2 37 1 169679199 SELL; SELL NM_000655; NR_029467 Body; TSS1500 cg06894723 1 37 13 110398142 cg06900229 1 37 17 48556928 RSAD1 NM_018346 Body chr17: 48556004-48556509 S_Shore cg06902609 2 37 7 985719 ADAP1 NM_006869 Body chr7: 985613-985913 Island cg06916315 1 37 5 174178587 chr5: 174178214-174178928 Island cg06996175 1 37 19 2546877 GNG7 NM_052847 5′UTR chr19: 2546620-2546983 Island cg07054668 1 37 3 52811637 ITIH1; ITIH1 NM_002215; NM_001166434 1stExon; TSS1500 cg07O61145 1 37 15 78556178 DNAJA4; DNAJA4 NM_018602; NM_001130182 TSS1500; TSS1500 chr15: 78556405-78557542 N_Shore cg07089698 1 37 3 5161802 chr3: 5163838-5164540 N_Shelf cg07102406 1 37 16 2294639 DCI NM_001919 Body cg07102406 3 37 16 2294639 DCI NM_001919 Body cg07115206 1 37 16 6425686 A2BP1; A2BP1 NM_001142333; NM_018723 5′UTR; 5′UTR cg07119830 1 37 10 104412306 TRIMS NM_030912 Body cg07139514 1 37 2 10665727 chr2: 10666541-10666765 N_Shore cg07145255 1 37 5 59995354 DEPDC1B; DEPDC1B NM_018369; NM_001145208 Body; Body chr5: 59995374-59996331 N_Shore cg07163173 1 37 2 67624373 ETAA1 NM_019002 TSS200 chr2: 67624372-67624844 Island cg07165115 1 37 2 82756475 cg07165756 1 37 11 66311422 ZDHHC24 NM_207340 Body chr11: 66313169-66313822 N_Shore cg07170752 1 37 1 225427173 DNAH14 NM_001373 Body cg07184658 2 37 9 96722329 chr9: 96720586-96723189 Island cg07190543 1 37 7 8261154 ICA1; ICA1; NM_004968; NM_001136020; Body; Body; ICA1 NM_022307 Body cg07216337 1 37 8 75233610 JPH1 NM_020647 TSS200 chr8: 75232649-75234101 Island cg07258847 2 37 6 66708570 cg07258847 6 37 6 66708570 cg07266964 1 37 2 135941054 cg07276861 1 37 4 76862355 NAAA; NAAA NM_014435; NM_001042402 TSS200; TSS200 chr4: 76861089-76862426 Island cg07288557 3 37 12 47226301 chr12: 47224912-47225664 S_Shore cg07304175 1 37 3 181414139 SOX2OT NR_004053 Body chr3: 181413014-181414022 S_Shore cg07321237 1 37 7 82754608 PCLO; PCLO NM_014510; NM_033026 Body; Body cg07331204 1 37 6 74998385 cg07367469 1 37 5 115988245 cg07379140 5 37 1 95538546 ALG14 NM_144988 TSS200 chr1: 95538251-95538551 Island cg07379140 1 37 1 95538546 ALG14 NM_144988 TSS200 chr1: 95538251-95538551 Island cg07476643 1 37 10 102729063 chr10: 102729299-102729710 N_Shore cg07483064 1 37 1 8938751 ENO1; ENO1 NM_001428; NM_001428 1stExon; 5′UTR chr1: 8938098-8939409 Island cg07487925 1 37 17 25620950 WSB1; WSB1 NM_015626; NM_134265 TSS200; TSS200 chr17: 25620999-25621730 N_Shore cg07493834 1 37 2 22114272 cg07499372 1 37 19 57631232 USP29 NM_020903 TSS1500 chr19: 57630339-57630633 S_Shore cg07517948 1 37 15 67801494 cg07549590 1 37 16 15018862 chr16: 15018805-15019032 Island cg07554478 1 37 3 113492074 ATP6V1A NM_001690 5′UTR cg07562918 2 37 9 21994435 CDKN2A; CDKN2BAS NM_058195; NR_003529 1stExon; TSS1500 chr9: 21994101-21995910 Island cg07576142 1 37 13 93879769 GPC6 NM_005708 1stExon chr13: 93879245-93880877 Island cg07581226 2 37 2 2939627 cg07588141 1 37 3 105588208 CBLB NM_170662 TSS1500 chr3: 105587279-105588218 Island cg07596845 1 37 6 82957841 IBTK NM_015525 TSS1500 chr6: 82957625-82957842 Island cg07602984 1 37 1 36790927 FAM176B NM_018166 TSS1500 chr1: 36786500-36789402 S_Shore cg07605410 1 37 1 16828163 chr1: 16825138-16826377 S_Shore cg07633317 1 37 16 49732623 ZNF423 NM_015069 Body chr16: 49732348-49732712 Island cg07695475 1 37 15 102358936 OR4F15 NM_001001674 1stExon cg07741793 1 37 17 26989030 SDF2; SUPT6H NM_006923; NM_003170 TSS200; TSS1500 chr17: 26988721-26989391 Island cg07743117 2 37 5 77146278 chr5: 77146998-77147785 N_Shore cg07749943 1 37 4 3468188 DOK7; DOK7 NM_173660; NM_001164673 Body; Body chr4: 3464799-3465440 S_Shelf cg07772660 1 37 1 17085863 MST1P9 NR_002729 Body chr1: 17085411-17086974 Island cg07772660 9 37 1 17085863 MST1P9 NR_002729 Body chr1: 17085411-17086974 Island cg07781162 1 37 17 74533951 CYGB NM_134268 TSS200 chr17: 74533281-74534566 Island cg07812819 1 37 7 89975908 GTPBP10; GTPBP10 NM_001042717; NM_033107 TSS200; TSS200 chr7: 89975785-89976027 Island cg07813249 1 37 4 46392253 GABRA2; GABRA2 NM_000807; NM_001114175 TSS200; TSS1500 chr4: 46391903-46392572 Island cg07813747 1 37 16 21514953 LOC100271836 NR_027155 TSS1500 chr16: 21512854-21513971 S_Shore cg07817024 1 37 1 119535500 chr1: 119535666-119535987 N_Shore cg07835814 1 37 20 32077669 CBFA2T2 NM_001032999 TSS1500 chr20: 32077657-32078469 Island cg07864467 1 37 10 134246595 cg07883117 1 37 7 101005846 EMID2 NM_133457 TSS1500 chr7: 101005899-101007443 N_Shore cg07908805 2 37 19 427022 SHC2 NM_012435 Body chr19: 426792-427819 Island cg07919744 1 37 15 52873609 KIAA1370 NM_019600 3′UTR cg07962315 1 37 9 77704473 OSTF1; C9orf95; NM_012383; NR023352; Body; TSS1500; chr9: 77702885-77703819 S_Shore C9orf95; C9orf95 NM_001127603; NM_017881 TSS1500; TSS1500 cg07966388 1 37 15 93363564 cg08028004 1 37 2 109336023 RANBP2; RANBP2 NM_006267; NM_006267 1stExon; 5′UTR chr2: 109335768-109336670 Island cg08035555 1 37 19 3558417 C19orf28; C19orf28; NM_021731; NM_001042680; TSS1500; TSS1500; chr19: 3556962-3558293 S_Shore C19orf28 NM_174983 TSS1500 cg08076266 1 37 2 120190202 TMEM37 NM_183240 Body chr2: 120190030-120190308 Island cg08237220 1 37 3 156332967 cg08242475 1 37 7 1327791 chr7: 1328525-1329029 N_Shore cg08269037 1 37 1 11751616 MAD2L2; C1orf187; NM_001127325; NM_198545; 5′UTR; TSS200; chr1: 11750701-11752651 Island MAD2L2 NM_001127325 1stExon cg08318726 1 37 12 114844265 TBX5; TBX5; NM_181486; NM_000192; TSS1500; 5′UTR; chr12: 114845861-114847650 N_Shore TBX5 NM_080717 5′UTR cg08356503 1 37 16 88105836 BANP; BANP NM_017869; NM_079837 Body; Body chr16: 88105640-88105908 Island cg08376824 1 37 20 5987738 CRLS1; CRLS1 NM_019095; NM_001127458 Body; TSS200 chr20: 5986399-5987297 S_Shore cg08447792 1 37 4 110600020 CCDC109B NM_017918 Body cg08453096 1 37 2 44065893 ABCG5; ABCG8; NM_022436; NM_022437; 5′UTR; TSS1500; ABCG5 NM_022436 1stExon cg08476757 1 37 3 107940931 IFT57 NM_018010 Body chr3: 107940930-107941503 Island cg08514765 2 37 16 58058888 MMP15 NM_002428 TSS1500 chr16: 58058712-58058928 Island cg08521684 1 37 3 195488725 MUC4; MUC4; NM_018406; NM_138297; Body; Body; chr3: 195488595-195489381 Island MUC4 NM_004532 Body cg08561442 1 37 16 49891857 chr16: 49888474-49893354 Island cg08592761 1 37 15 71146185 LARP6; LARP6 NM_197958; NM_018357 Body; Body chr15: 71145995-71146820 Island cg08623277 1 37 2 206004876 PARD3B; PARD3B; NM_152526; NM_057177; Body; Body; PARD3B NM_205863 Body cg08643994 1 37 4 141500606 cg08658621 1 37 10 133999287 DPYSL4 NM_006426 TSS1500 chr10: 133998912-134001500 Island cg08671647 1 37 4 30724564 PCDH7; PCDH7; NM_032456; NM_032457; 1stExon; Body; chr4: 30721204-30724842 Island PCDH7 NM_002589 1stExon cg08671647 2 37 4 30724564 PCDH7; PCDH7; NM_032456; NM_032457; 1stExon; Body; chr4: 30721204-30724842 Island PCDH7 NM_002589 1stExon cg08727867 1 37 21 15588349 RBM11 NM_144770 TSS200 chr21: 15588439-15588908 N_Shore cg08728848 6 37 17 30437958 cg08728848 3 37 17 30437958 cg08751971 1 37 7 128587827 IRF5; IRF5; NM_032643; NM_001098629; Body; Body; IRF5; IRF5; NM_001098628; NM_001098631; Body; Body; IRF5; IRF5; NM_001098630; NM_001098627; Body; Body; IRF5 NM_002200 Body cg08753297 2 37 6 56716612 DST; DST; NM_001144771; NM_001144770; TSS200; 5′UTR; DST; DST NM_001144770; NM_001144769 1stExon; Body cg08782158 4 37 2 927755 cg08813539 1 37 10 29011452 chr10: 29011053-29011453 Island cg08852245 1 37 4 175138785 chr4: 175135259-175135496 S_Shelf cg08864035 3 37 1 114471711 HIPK1; HIPK1 NM_198268; NM_152696 TSS1500; TSS1500 chr1: 114471965-114472899 N_Shore cg08866633 1 37 13 113968514 LAMP1 NM_005561 Body cg08891883 1 37 4 8347266 chr4: 8347476-8347889 N_Shore cg08905496 3 37 1 165414332 RXRG; RXRG; NM_001009598; NM_006917; 5′UTR; 5′UTR; RXRG; RXRG NM_006917; NM_001009598 1stExon; 1stExon cg08943292 1 37 4 40337370 CHRNA9 NM_017581 TSS200 cg08983429 1 37 16 3577455 CLUAP1; CLUAP1 NM_015041; NM_024793 Body; Body cg08992729 1 37 6 32809425 PSMB8; PSMB8 NM_004159; NM_148919 Body; Body chr6: 32811494-32811839 N_Shelf cg09032973 1 37 5 140165998 PCDHA1; PCDHA1; NM_031410; NM_031411; 1stExon; 1stExon; chr5: 140165958-140166214 Island PCDHA1 NM_018900 1stExon cg09119967 1 37 20 9494838 C20orf103 NM_012261 TSS1500 chr20: 9495253-9495597 N_Shore cg09214993 1 37 15 64673618 KIAA0101; KIAA0101; NM_001029989; NM_014736; 1stExon; 1stExon; KIAA0101; KIAA0101 NM_001029989; NM_014736 5′UTR; 5′UTR cg09222892 1 37 1 25734099 RHCE; RHCE; NM_138616; NM_138617; Body; Body; Body; RHCE; RHCE NM_138618; NM_020485 Body cg09272909 1 37 9 71736999 TJP2 NM_001170414 5′UTR chr9: 71736074-71737367 Island cg09292409 2 37 16 15461083 cg09334915 1 37 1 239450936 cg09343402 1 37 19 24216269 cg09365557 1 37 17 59477564 TBX2 NM_005994 1stExon chr17: 59473060-59483266 Island cg09413529 1 37 12 115112225 TBX3; TBX3 NM_005996; NM_016569 Body; Body chr12: 115112014-115112627 Island cg09418673 3 37 11 76372128 LRRC32; LRRC32 NM_001128922; NM_005512 Body; Body cg09418673 4 37 11 76372128 LRRC32; LRRC32 NM_001128922; NM_005512 Body; Body cg09463211 1 37 15 99093248 chr15: 99091355-99091812 S_Shore cg09499421 1 37 16 31020735 STX1B NM_052874 Body cg09507411 1 37 5 82395650 XRCC4; XRCC4; NM_022550; NM_003401; 5′UTR; 5′UTR; XRCC4 NM_022406 5′UTR cg09600829 2 37 9 96216052 FAM120A; FAM120AOS NM_014612; NM_198841 Body; TSS200 chr9: 96213340-96214953 S_Shore cg09653641 1 37 7 92455499 CDK6; CDK6 NM_001259; NM_001145306 Body; Body cg09672383 2 37 2 25390540 POMC; POMC NM_000939; NM_001035256 5′UTR; 5′UTR chr2: 25391072-25391875 N_Shore cg09672383 1 37 2 25390540 POMC; POMC NM_000939; NM_001035256 5′UTR; 5′UTR chr2: 25391072-25391875 N_Shore cg09717927 1 37 13 112630399 chr13: 112630568-112630796 N_Shore cg09788029 3 37 12 103004347 cg09814034 1 37 20 44876346 CDH22 NM_021248 Body chr20: 44875253-44875454 S_Shore cg09822136 1 37 5 14144123 TRIO NM_007118 Body chr5: 14143017-14145350 Island cg09952395 1 37 11 63258712 HRASLS5; HRASLS5; NM_001146728; NM_001146729; TSS200; TSS200; chr11: 63258378-63258804 Island HRASLS5 NM_054108 TSS200 cg10006235 2 37 11 49226370 FOLH1; FOLH1 NM_004476; NM_001014986 Body; Body chr11: 49229717-49230040 N_Shelf cg10045446 1 37 7 32530734 LSM5; LSM5; NM_001139499; NM_012322; 5′UTR; TSS1500; chr7: 32529753-32530146 S_Shore LSM5; LSM5 NR_024466; NM_001130710 TSS1500; 5′UTR cg10045446 2 37 7 32530734 LSM5; LSM5; NM_001139499; NM_012322; 5′UTR; TSS1500; chr7: 32529753-32530146 S_Shore LSM5; LSM5 NR_024466; NM_001130710 TSS1500; 5′UTR cg10077985 1 37 10 833127 cg10091458 3 37 9 116858634 KIF12 NM_138424 Body chr9: 116860473-116860695 N_Shore cg10128416 1 37 1 75198403 TYW3; CRYZ; NM_001162916; NM_001130042; TSS1500; 5′UTR; CRYZ; TYW3; NM_001130043; NR_027962; 5′UTR; TSS1500; TYW3; CRYZ; NM_138467; NM_001134759; TSS1500; 5′UTR; CRYZ NM_001889 5′UTR cg10159215 1 37 1 99470560 LPPR5; LPPR5 NM_001010861; NM_001037317 TSS200; TSS200 chr1: 99469932-99470968 Island cg10174031 1 37 16 31408898 ITGAD NM_005353 Body cg10202874 1 37 16 32165225 HERC2P4 NR_002827 TSS1500 cg10206440 4 37 1 16353594 CLCNKA; CLCNKA NM_001042704; NM_004070 Body; Body cg10206440 1 37 1 16353594 CLCNKA; CLCNKA NM_001042704; NM_004070 Body; Body cg10211414 1 37 1 8875053 RERE; RERE NM_012102; NM_001042681 5′UTR; 5′UTR chr1: 8877012-8877283 N_Shore cg10211414 1 37 1 8875053 RERE; RERE NM_012102; NM_001042681 5′UTR; 5′UTR chr1: 8877012-8877283 N_Shore cg10261325 1 37 10 29874759 SVIL; SVIL NM_021738; NM_003174 5′UTR; 5′UTR cg10261325 1 37 10 29874759 SVIL; SVIL NM_021738; NM_003174 5′UTR; 5′UTR cg10306485 7 37 13 114881556 RASA3 NM_007368 Body chr13: 114879041-114879530 S_Shelf cg10306485 3 37 13 114881556 RASA3 NM_007368 Body chr13: 114879041-114879530 S_Shelf cg10368533 1 37 12 22778127 ETNK1; ETNK1 NM_001039481; NM_018638 1stExon; 1stExon chr12: 22777988-22778301 Island cg10368935 1 37 10 18240316 SLC39A12; SLC39A12 NM_001145195; NM_152725 TSS1500; TSS1500 cg10405239 1 37 17 26733360 SLC46A1 NM_080669 TSS200 chr17: 26732812-26733396 Island cg10423227 1 37 2 64752200 AFTPH; AFTPH; NM_203437; NM_001002243; 5′UTR; 5′UTR; chr2: 64751141-64752083 S_Shore AFTPH NM_017657 5′UTR cg10490795 1 37 5 150035893 SYNPO NM_007286 Body chr5: 150035968-150036629 N_Shore cg10514235 1 37 4 15003844 chr4: 15003059-15006761 Island cg10579818 1 37 19 34117242 CHST8; CHST8 NM_001127895; NM_001127896 5′UTR; 5′UTR chr19: 34112279-34114353 S_Shelf cg10596590 1 37 6 51814836 PKHD1; PKHD1 NM_138694; NM_170724 Body; Body cg10601972 1 37 3 12851576 CAND2; CAND2 NM_001162499; NM_012298 Body; Body chr3: 12851516-12851823 Island cg10607939 1 37 7 112091280 IFRD1JFRD1 NM_001550; NM_001007245 Body; Body chr7: 112090122-112091412 Island cg10609068 4 37 12 45609265 ANO6; ANO6; NM_001142680; NM_001142679; TSS1500; TSS1500; chr12: 45609713-45610752 N_Shore PLEKHA9; ANO6 NM_015899; NM_001025356 5′UTR; TSS1500 cg10609068 1 37 12 45609265 ANO6; ANO6; NM_001142680; NM_001142679; TSS1500; TSS1500; chr12: 45609713-45610752 N_Shore PLEKHA9; ANO6 NM_015899; NM_001025356 5′UTR; TSS1500 cg10674754 4 37 4 8456019 C4orf23 NM_152544 TSS200 cg10674754 3 37 4 8456019 C4orf23 NM_152544 TSS200 cg10688514 1 37 10 48354852 ZNF488 NM_153034 TSS1500 chr10: 48354459-48355197 Island cg10703619 1 37 7 155014511 cg10711996 1 37 10 32635917 EPC1; EPC1 NM_025209; NM_025209 5′UTR; 1stExon chr10: 32635217-32636655 Island cg10722444 1 37 13 112630569 chr13: 112630568-112630796 Island cg10776643 1 37 14 71527576 PCNX NM_014982 Body cg10842913 1 37 12 125755229 cg10843276 1 37 4 726697 PCGF3 NM_006315 5′UTR chr4: 724335-726070 S_Shore cg10895973 1 37 17 14212636 HS3ST3B1 NM_006041 Body chr17: 14212363-14212788 Island cg10902101 1 37 22 48899955 FAM19A5 NM_001082967 Body chr22: 48896375-48896591 S_Shelf cg10909154 1 37 16 2723619 chr16: 2722923-2723674 Island cg10932815 1 37 12 68294240 cg10966582 1 37 1 17085860 MST1P9 NR_002729 Body chr1: 17085411-17086974 Island cg10966582 5 37 1 17085860 MST1P9 NR_002729 Body chr1: 17085411-17086974 Island cg10988062 1 37 7 64023434 ZNF680; ZNF680; NM_001130022; NM_178558; 1stExon; 5′UTR; ZNF680; ZNF680 NM_178558; NM_001130022 1stExon; 5′UTR cg11005250 3 37 12 108297742 chr12: 108297426-108297743 Island cg11084629 1 37 1 55230770 PARS2 NM_152268 TSS1500 chr1: 55229992-55230369 S_Shore cg11104313 1 37 3 111717534 TAGLN3; TAGLN3; NM_013259; NM_001008272; TSS200; TSS200; TAGLN3 NM_001008273 TSS1500 cg11159141 1 37 3 11529333 ATG7; ATG7; NM_001136031; NM_001144912; Body; Body; chr3: 11529784-11530120 N_Shore ATG7 NM_006395 Body cg11199172 1 37 17 46707338 chr17: 46710812-46711419 N_Shelf cg11203397 1 37 13 46870454 cg11222065 1 37 6 33240468 VPS52; RPS18 NM_022553; NM_022551 TSS1500; Body chr6: 33239326-33240099 S_Shore cg11273848 1 37 10 130506845 chr10: 130508443-130508658 N_Shore cg11303425 1 37 12 6798826 ZNF384; ZNF384; NM_001039916; NM_001039920; TSS1500; TSS200; ZNF384; ZNF384; NM_001135734; NM_001039918; TSS200; TSS1500; ZNF384; ZNF384; NM_001039917; NM_133476; TSS200; TSS1500; ZNF384 NM_001039919 TSS200 cg11322849 1 37 11 2182783 INS; INS-IGF2; NM_000207; NR_003512; TSS1500; TSS1500; INS-IGF2 NM_001042376 TSS1500 cg11336643 1 37 12 124432686 CCDC92 NM_025140 5′UTR cg11350208 1 37 2 133033202 cg11386711 1 37 3 186651116 ST6GAL1; ST6GAL1 NM_173216; NM_173217 5′UTR; 5′UTR chr3: 186648174-186649103 S_Shelf cg11461030 1 37 1 46932239 chr1: 46932130-46932892 Island cg11461302 1 37 22 38507451 BAIAP2L2 NM_025045 TSS1500 cg11498652 2 37 5 40834691 RPL37 NM_000997 Body chr5: 40835241-40835873 N_Shore cg11542394 2 37 15 101419011 ALDH1A3 NM_000693 TSS1500 chr15: 101419261-101421133 N_Shore cg11551464 3 37 8 49595738 cg11553116 1 37 6 2871823 chr6: 2875601-2875811 N_Shelf cg11575929 1 37 6 28414894 cg11677722 1 37 19 39881393 MED29; PAF1 NM_017592; NM_019088 TSS1500; Body chr19: 39881332-39882164 Island cg11723795 1 37 14 91975931 SMEK1 NM_032560 Body chr14: 91975670-91977326 Island cg11746846 3 37 18 3067337 MYOM1; MYOM1 NM_019856; NM_003803 Body; Body chr18: 3067297-3067533 Island cg11746846 1 37 18 3067337 MYOM1; MYOM1 NM_019856; NM_003803 Body; Body chr18: 3067297-3067533 Island cg11750736 1 37 17 10634140 TMEM220 NM_001004313 TSS1500 chr17: 10632789-10633490 S_Shore cg11781564 1 37 5 73016764 RGNEF NM_001080479 Body cg11801727 1 37 1 228659093 chr1: 228658937-228659152 Island cg11832722 1 37 18 28623060 DSC3; DSC3 NM_001941; NM_024423 TSS1500; TSS1500 chr18: 28621489-28623117 Island cg11865413 15 37 10 72969054 chr10: 72972075-72973895 N_Shelf cg11865413 9 37 10 72969054 chr10: 72972075-72973895 N_Shelf cg11958128 1 37 12 3226445 TSPAN9; TSPAN9 NM_001168320; NM_006675 5′UTR; 5′UTR cg12000587 1 37 17 30186630 C17orf79 NM_018405 TSS1500 chr17: 30185764-30186580 S_Shore cg12014145 1 37 16 30346812 LOC595101 NR_002453 TSS200 chr16: 30346052-30346865 Island cg12015279 1 37 18 55318716 ATP8B1 NM_005603 Body chr18: 55315730-55315932 S_Shelf cg12041387 2 37 7 96650171 DLX5 NM_005221 Body chr7: 96650221-96651551 N_Shore cg12068833 1 37 4 132896266 chr4: 132896360-132896778 N_Shore cg12068833 1 37 4 132896266 chr4: 132896360-132896778 N_Shore cg12071328 1 37 11 20690930 NELL1; NELL1 NM_201551; NM_006157 TSS200; TSS200 chr11: 20690579-20691845 Island cg12102432 1 37 11 119378641 cg12226306 1 37 3 105087718 ALCAM NM_001627 Body chr3: 105088072-105088339 N_Shore cg12226306 1 37 3 105087718 ALCAM NM_001627 Body chr3: 105088072-105088339 N_Shore cg12243858 1 37 7 149473178 SSPO NM_198455 1stExon chr7: 149469542-149469748 S_Shelf cg12285737 1 37 19 49931759 chr19: 49931203-49931804 Island cg12329460 1 37 10 105992247 C10orf79 NM_025145 TSS200 chr10: 105991899-105992248 Island cg12378753 1 37 10 116527201 chr10: 116527524-116528474 N_Shore cg12400434 1 37 5 1491377 LPCAT1 NM_024830 Body chr5: 1489799-1490071 S_Shore cg12458866 1 37 1 9353610 SPSB1 NM_025106 5′UTR cg12466737 2 37 18 35146589 BRUNOL4; BRUNOL4; NM_001025089; NM_001025087; TSS1500; TSS1500; chr18: 35144907-35147628 Island BRUNOL4; BRUNOL4 NM_020180; NM_001025088 TSS1500; TSS1500 cg12467960 2 37 11 68201194 LRP5 NM_002335 Body chr11: 68201118-68201321 Island cg12473849 1 37 3 136882749 cg12489353 1 37 19 48231499 EHD2 NM_014601 Body chr19: 48229072-48229507 S_Shore cg12494529 1 37 10 1082432 C10orf110; C10orf110; NR_024629; NR_027708; Body; Body; C10orf110; C10orf110 NR_027709; NR_024628 Body; Body cg12512039 1 37 7 65958832 chr7: 65958470-65959121 Island cg12522342 2 37 17 64831573 chr17: 64831193-64831574 Island cg12532563 1 37 4 83956223 COPS4 NM_016129 TSS200 cg12568669 1 37 8 11666485 FDFT1 NM_004462 Body chr8: 11665773-11666045 S_Shore cg12583367 1 37 4 4412229 D4S234E; D4S234E NM_014392; NM_001040101 Body; Body cg12624829 2 37 10 106113175 CCDC147 NM_001008723 TSS1500 cg12791476 1 37 7 44059249 POLR2J4 NR_003655 TSS1500 chr7: 44058608-44058988 S_Shore cg12797594 1 37 22 36236395 RBM9; RBM9; NM_014309; NM_001082578; 5′UTR; Body; RBM9; RBM9; NM_001082579; NM_001082576; Body; 5′UTR; RBM9; RBM9; NM_001031695; NM_001031695; 5′UTR; 1stExon; RBM9; RBM9; NM_001082576; NM_014309; 1stExon; 1stExon; RBM9; RBM9 NM_001082577; NM_001082577 5′UTR; 1stExon cg12822242 1 37 8 127572993 chr8: 127568676-127570873 S_Shelf cg12877889 1 37 3 21446874 VENTXP7 NR_002311 TSS1500 cg12934366 2 37 8 1960466 chr8: 1956926-1957177 S_Shelf cg13016524 1 37 11 16628944 chr11: 16626053-16629180 Island cg13066016 1 37 1 63786083 chr1: 63782394-63790471 Island cg13074470 1 37 3 126854308 chr3: 126854106-126854848 Island cg13112361 1 37 11 63258739 HRASLS5; HRASLS5; NM_001146728; NM_001146729; TSS200; TSS200; chr11: 63258378-63258804 Island HRASLS5 NM_054108 TSS200 cg13130934 1 37 15 25449922 SNORD115-21; SNORD115-20; NR_003313; NR_003312; TSS1500; TSS1500; SNORD115-15 NR_003307 TSS1500 cg13193962 2 37 4 156875105 CTSO NM_001334 TSS200 chr4: 156874740-156875083 S_Shore cg13209388 1 37 1 6355060 ACOT7; ACOT7; NM_181864; NM_181865; Body; Body; ACOT7; ACOT7 NM_007274; NM_181866 Body; Body cg13229233 1 37 17 67326602 chr17: 67322709-67323837 S_Shelf cg13229345 1 37 4 187984633 chr4: 187984505-187984762 Island cg13230424 2 37 17 45930033 SP6 NM_199262 5′UTR chr17: 45928211-45928710 S_Shore cg13230424 3 37 17 45930033 SP6 NM_199262 5′UTR chr17: 45928211-45928710 S_Shore cg13279956 1 37 11 55653268 SPRYD5 NM_032681 Body cg13286318 1 37 8 57906058 IMPAD1 NM_017813 1stExon chr8: 57905700-57906452 Island cg13306164 1 37 1 33352184 HPCA NM_002143 5′UTR chr1: 33351686-33352397 Island cg13312403 1 37 8 71246470 NCOA2 NM_006540 5′UTR cg13401339 1 37 2 24272928 FKBP1B; FKBP1B NM_054033; NM_004116 Body; Body chr2: 24272582-24273313 Island cg13411336 1 37 11 43968842 chr11: 43963626-43966048 S_Shelf cg13424673 2 37 1 50489744 AGBL4 NM_032785 TSS200 chr1: 50489417-50489846 Island cg13426079 3 37 1 41284948 KCNQ4; KCNQ4 NM_004700; NM_172163 Body; Body chr1: 41284847-41285149 Island cg13462158 3 37 1 55522104 PCSK9 NM_174936 Body cg13473576 1 37 7 97601586 MGC72080 NR_002822 Body chr7: 97601307-97601813 Island cg13488605 2 37 19 38908709 RASGRP4; RASGRP4; NM_001146205; NM_001146207; Body; Body; chr19: 38908487-38909240 Island RASGRP4; RASGRP4; NM_001146204; NM_170604; Body; Body; RASGRP4; RASGRP4; NM_001146202; NM_001146203; Body; Body; RASGRP4 NM_001146206 Body cg13523386 1 37 4 71457838 AMBN NM_016519 TSS200 cg13560904 1 37 1 149982854 OTUD7B NM_020205 TSS200 chr1: 149982153-149982860 Island cg13565382 1 37 10 63628787 cg13565382 4 37 10 63628787 cg13568258 1 37 19 48823427 CCDC114 NM_144577 TSS200 chr19: 48824529-48825493 N_Shore cg13605988 1 37 15 45421612 DUOX1; DUOX1; NM_175940; NM_017434; TSS1500; TSS1500; chr15: 45421236-45422394 Island DUOXA1 NM_144565 5′UTR cg13612295 1 37 18 72124791 FAM69C NM_001044369 TSS1500 chr18: 72123606-72124717 S_Shore cg13614440 2 37 17 76471012 DNAH17 NM_173628 Body chr17: 76472296-76472533 N_Shore cg13648344 1 37 9 36328161 cg13663218 1 37 12 72666976 LOC283392; TRHDE; NR_026837; NM_013381; Body; 1stExon; chr12: 72665683-72667551 Island LOC283392 NR_026836 Body cg13667739 1 37 14 105944604 CRIP2 NM_001312 Body chr14: 105944421-105945700 Island cg13667739 1 37 14 105944604 CRIP2 NM_001312 Body chr14: 105944421-105945700 Island cg13684188 1 37 9 135282273 TTF1 NM_007344 TSS200 chr9: 135282052-135282315 Island cg13686622 1 37 13 41634589 WBP4 NM_007187 TSS1500 chr13: 41634172-41636120 Island cg13857186 1 37 9 116173257 C9orf43; POLE3; NM_152786; NR_027261; 5′UTR; TSS1500; chr9: 116172303-116173090 S_Shore C9orf43; POLE3 NM_152786; NM_017443 1stExon; TSS1500 cg13861904 1 37 9 139428006 NOTCH1 NM_017617 Body chr9: 139428318-139428527 N_Shore cg13892902 1 37 15 43478040 CCNDBP1; CCNDBP1; NM_037370; NM_012142; TSS200; Body; chr15: 43477588-43477816 S_Shore CCNDBP1; CCNDBP1 NR_027513; NR_027514 Body; Body cg13896879 1 37 1 150785718 ARNT; ARNT; NM_178427; NM_001668; Body; Body; ARNT NM_178426 Body cg13918350 1 37 7 1153507 C7orf50; C7orf50; NM_001134395; NM_032350; Body; Body; chr7: 1155303-1157445 N_Shore C7orf50 NM_001134396 Body cg13918350 1 37 7 1153507 C7orf50; C7orf50; NM_001134395; NM_032350; Body; Body; chr7: 1155303-1157445 N_Shore C7orf50 NM_001134396 Body cg13944505 1 37 1 187460781 cg13995006 1 37 8 118532813 MED30 NM_080651 TSS200 chr8: 118532855-118533311 N_Shore cg13999514 1 37 7 106302548 FLJ36031 NM_175884 TSS1500 chr7: 106300402-106301573 S_Shore cg14022105 2 37 11 78288793 chr11: 78285405-78285995 S_Shelf cg14022105 3 37 11 78288793 chr11: 78285405-78285995 S_Shelf cg14048880 1 37 9 139069897 chr9: 139069755-139070076 Island cg14056644 1 37 4 111559105 PITX2; PITX2 NM_153427; NM_153426 TSS1500; TSS1500 chr4: 111560563-111560808 N_Shore cg14097440 1 37 14 74251018 C14orf43 NM_001043318 5′UTR chr14: 74253387-74254188 N_Shelf cg14109799 2 37 14 31495427 AP4S1; STRN3; NM_007077; NM_014574; 5′UTR; 1stExon; STRN3; STRN3; NM_014574; NM_001083893; 5′UTR; 1stExon; STRN3; AP4S1 NM_001083893; NM_001128126 5′UTR; 5′UTR cg14157578 1 37 9 110764967 cg14185808 1 37 2 105653893 MRPS9 NM_182640 TSS1500 chr2: 105654249-105654771 N_Shore cg14200609 1 37 12 94853950 CCDC41; CCDC41; NM_016122; NM_001042399; TSS200; TSS200; chr12: 94853336-94854307 Island LOC144486 NR_027035 Body cg14237674 1 37 17 43239170 HEXIM2 NM_144608 5′UTR chr17: 43238260-43239233 Island cg14249856 1 37 7 77167329 PTPN12; PTPN12; NM_001131009; NM_001131008; TSS200; TSS200; chr7: 77166610-77167337 Island PTPN12 NM_002835 Body cg14279842 2 37 14 50159788 KLHDC1 NM_172193 TSS200 chr14: 50159667-50160424 Island cg14280905 5 37 9 136424187 ADAMTSL2; ADAMTSL2 NM_014694; NM_001145320 Body; Body chr9: 136426124-136426390 N_Shore cg14294250 3 37 17 1957154 HIC1 NM_006497 TSS1500 chr17: 1952919-1962328 Island cg14314896 1 37 19 430690 SHC2 NM_012435 Body chr19: 429260-429581 S_Shore cg14330460 4 37 6 168559427 cg14330460 7 37 6 168559427 cg14351127 1 37 9 102956206 INVS; INVS NM_014425; NM_183245 Body; Body cg14361033 1 37 9 124981504 LHX6; LHX6 NM_199160; NM_014368 Body; Body chr9: 124981535-124982835 N_Shore cg14397696 1 37 13 105792284 cg14414764 1 37 8 67741966 SGK3; SGK3; NM_170709; NM_001033578; Body; Body; SGK3 NM_013257 Body cg14447152 1 37 9 140153393 COBRA1 NM_015456 Body chr9: 140149205-140150502 S_Shelf cg14447152 2 37 9 140153393 COBRA1 NM_015456 Body chr9: 140149205-140150502 S_Shelf cg14455170 1 37 13 42002398 cg14466759 1 37 7 101518899 CUX1; CUX1; NM_181500; NM_181552; Body; Body; CUX1 NM_001913 Body cg14466759 1 37 7 101518899 CUX1; CUX1; NM_181500; NM_181552; Body; Body; CUX1 NM_001913 Body cg14467066 1 37 17 79419739 BAHCC1 NM_001080519 Body chr17: 79420144-79420437 N_Shore cg14482093 1 37 8 22461488 KIAA1967; C8orf58; NM_021174; NM_001013842; TSS1500; 3′UTR; chr8: 22462092-22462868 N_Shore KIAA1967 NM_199205 TSS1500 cg14540650 1 37 9 6683274 chr9: 6680856-6681758 S_Shore cg14543412 1 37 6 26224100 HIST1H3E NM_003532 TSS1500 chr6: 26225386-26225790 N_Shore cg14555127 3 37 7 35841578 SEPT7; SEPT7 NM_001011553; NM_001788 Body; Body chr7: 35840132-35841591 Island cg14616423 7 37 9 16315271 cg14616423 1 37 9 16315271 cg14639163 1 37 2 219738529 WNT6 NM_006522 Body chr2: 219738081-219738788 Island cg14657159 2 37 12 56211136 ORMDL2; SARNP; NM_014182; NR_026723; TSS1500; Body; chr12: 56211325-56211553 N_Shore SARNP; SARNP NR_026722; NM_033082 Body; Body cg14710040 4 37 19 3985464 EEF2 NM_001961 TSS200 chr19: 3984962-3985722 Island cg14737877 1 37 8 664783 ERICH1 NM_207332 Body chr8: 663998-664794 Island cg14780600 1 37 2 240281345 HDAC4 NM_006037 5′UTR cg14795305 2 37 7 150974453 SMARCD3; SMARCD3 NM_001003802; NM_003078 TSS1500; TSS1500 chr7: 150974116-150974535 Island cg14834675 1 37 12 70083105 BEST3; BEST3 NM_032735; NM_152439 Body; TSS200 cg14857851 1 37 3 15115139 ZFYVE20 NM_022340 3′UTR chr3: 15116003-15116219 N_Shore cg14858469 1 37 15 96874050 NR2F2; NR2F2 NM_021005; NM_001145155 TSS200; Body chr15: 96873408-96877721 Island cg14866032 1 37 15 98195808 chr15: 98196021-98196391 N_Shore cg14870156 1 37 6 33048540 HLA-DPB1 NM_002121 Body chr6: 33048416-33048814 Island cg14871601 1 37 7 64030039 chr7: 64029902-64030972 Island cg14877741 1 37 9 125703099 RABGAP1 NM_012197 TSS200 chr9: 125703098-125703597 Island cg14938587 1 37 7 155790392 cg14965968 1 37 3 44803235 KIF15; KIF15; NM_020242; NM_020242; 1stExon; 5′UTR; chr3: 44802852-44803618 Island KIAA1143 NM_020696 TSS200 cg15002362 1 37 6 129796899 LAMA2; LAMA2 NM_001079823; NM_000426 Body; Body cg15002362 1 37 6 129796899 LAMA2; LAMA2 NM_001079823; NM_000426 Body; Body cg15002580 1 37 8 98636815 chr8: 98636694-98636904 Island cg15025054 2 37 1 212964885 TATDN3; NSL1; NM_00U46171; NM_015471; TSS1500; 1stExon; chr1: 212964866-212965347 Island TATDN3; NSL1; NM_001042553; NM_001042549; TSS1500; 1stExon; TATDN3; TATDN3; NM_001042552; NM_001146170; TSS1500; TSS1500; TATDN3 NM_001146169 TSS1500 cg15109571 2 37 10 104264023 SUFU NM_016169 1stExon chr10: 104263676-104264155 Island cg15119076 1 37 19 19976606 ZNF253 NM_021047 TSS200 cg15140902 1 37 6 21667815 FLJ22536 NR_015410 Body chr6: 21665715-21666031 S_Shore cg15196058 1 37 4 130934318 cg15228928 2 37 13 112727521 chr13: 112726281-112728419 Island cg15330255 1 37 10 103454985 FBXW4 NM_022039 TSS1500 chr10: 103454126-103454478 S_Shore cg15333277 2 37 8 41733931 ANK1 NM_001142446 Body chr8: 41733535-41733911 S_Shore cg15347484 2 37 2 79515194 cg15490897 1 37 1 55038020 ACOT11; ACOT11 NM_015547; NM_147161 Body; Body cg15518950 1 37 5 72415770 TMEM171; TMEM171 NM_001161342; NM_173490 TSS1500; TSS1500 chr5: 72415611-72416766 Island cg15554438 1 37 11 92931280 SLC36A4 NM_152313 TSS200 chr11: 92930760-92931391 Island cg15590056 1 37 7 149732579 cg15595333 1 37 11 117689733 cg15602420 1 37 1 20205059 chr1: 20208807-20209462 N_Shelf cg15651394 1 37 2 36584981 CRIM1 NM_016441 Body chr2: 36584500-36584982 Island cg15681626 1 37 11 64739253 chr11: 64739010-64739750 Island cg15685834 1 37 1 18970180 PAX7; PAX7; NM_013945; NM_002584; Body; Body; chr1: 18969548-18970739 Island PAX7 NM_001135254 Body cg15705470 1 37 5 87972265 LOC645323; LOC645323 NR_024383; NR_015436 Body; Body chr5: 87973951-87974294 N_Shore cg15709065 1 37 3 134090737 AMOTL2 NM_016201 5′UTR chr3: 134092257-134093741 N_Shore cg15714041 1 37 9 32384344 ACO1 NM_002197 TSS1500 chr9: 32384420-32384911 N_Shore cg15745910 1 37 13 112874219 cg15750986 1 37 7 98249103 NPTX2 NM_002523 Body chr7: 98245805-98247759 S_Shore cg15760840 1 37 7 27225222 HOXA11AS; HOXA11 NR_002795; NM_005523 Body; TSS1500 chr7: 27225050-27225629 Island cg15810744 1 37 11 67211300 CORO1B; CORO1B NM_001018070; NM_020441 TSS200; TSS1500 cg15812873 1 37 16 28635015 SULT1A1 NM_177536 TSS200 chr16: 28634440-28635031 Island cg15840462 1 37 1 969744 AGRN NM_198576 Body chr1: 967966-970238 Island cg15846886 1 37 17 79790116 FAM195B; FAM195B NM_207368; NM_001093767 5′UTR; 5′UTR chr17: 79790530-79791553 N_Shore cg15877233 1 37 7 40611688 C7orf10 NM_024728 Body cg15892650 1 37 5 150524635 ANXA6; ANXA6 NM_001155; NM_004033 Body; Body cg15913680 3 37 11 72353343 PDE2A; PDE2A; NM_001143839; NR026572; 1stExon; Body; chr11: 72353222-72354358 Island PDE2A; PDE2A NM_001146209; NM_002599 Body; Body cg15917344 1 37 7 89975873 GTPBP10; GTPBP10 NM_001042717; NM_033107 TSS200; TSS200 chr7: 89975785-89976027 Island cg15959921 1 37 4 8702279 cg15974085 1 37 18 71815641 C18orf55; FBXO15; NM_014177; NM_152676; TSS200; TSS1500; chr18: 71814555-71815716 Island FBXO15 NM_001142958 TSS1500 cg15974085 15 37 18 71815641 C18orf55; FBXO15; NM_014177; NM_152676; TSS200; TSS1500; chr18: 71814555-71815716 Island FBXO15 NM_001142958 TSS1500 cg15994467 1 37 12 52401523 GRASP NM_181711 Body chr12: 52400467-52401696 Island cg16000637 1 37 7 1274142 UNCX NM_001080461 Body chr7: 1269165-1282864 Island cg16001460 3 37 6 57181802 PRIM2 NM_000947 TSS1500 cg16001460 8 37 6 57181802 PRIM2 NM_000947 TSS1500 cg16009381 2 37 5 173043599 BOD1; BOD1; NM_138369; NM_138369; 5′UTR; 1stExon; chr5: 173043123-173043895 Island BOD1; BOD1 NM_001159651; NM_001159651 5′UTR; 1stExon cg16009381 1 37 5 173043599 BOD1; BOD1; NM_138369; NM_138369; 5′UTR; 1stExon; chr5: 173043123-173043895 Island BOD1; BOD1 NM_001159651; NM_001159651 5′UTR; 1stExon cg16013630 2 37 1 1406606 ATAD3B NM_031921 TSS1500 chr1: 1406844-1407821 N_Shore cg16026088 1 37 9 132565261 TOR1B NM_014506 TSS200 chr9: 132565316-132566033 N_Shore cg16060163 3 37 17 80454814 chr17: 80454652-80455632 Island cg16084014 1 37 7 114585003 MDFIC; MDFIC NM_199072; NM_001166345 Body; Body cg16091269 1 37 3 197183271 chr3: 197183404-197183724 N_Shore cg16091269 1 37 3 197183271 chr3: 197183404-197183724 N_Shore cg16101346 1 37 1 186650479 PTGS2 NM_000963 TSS1500 chr1: 186649310-186650081 S_Shore cg16101636 1 37 6 29711438 LOC285830; LOC285830 NR_026972; NR_026973 Body; Body cg16101636 1 37 6 29711438 LOC285830; LOC285830 NR_026972; NR_026973 Body; Body cg16121685 5 37 1 162467625 UHMK1 NM_175866 TSS200 chr1: 162467599-162468027 Island cg16143319 1 37 2 32230813 MEMO1; MEMO1 NM_015955; NM_001137602 Body; Body chr2: 32234653-32236248 N_Shelf cg16208269 1 37 3 45665937 LIMD1 NM_014240 Body cg16226310 1 37 5 843633 ZDHHC11 NM_024786 Body chr5: 843458-843767 Island cg16226310 1 37 5 843633 ZDHHC11 NM_024786 Body chr5: 843458-843767 Island cg16233210 1 37 3 171778391 FNDC3B; FNDC3B NM_022763; NM_001135095 5′UTR; 5′UTR cg16234298 1 37 22 17091297 psiTPTE22 NR_001591 Body chr22: 17090455-17091224 S_Shore cg16271221 1 37 3 188656237 cg16315155 1 37 19 55249794 KIR2DL3; KIR2DL3 NM_015868; NM_014511 TSS200; TSS200 cg16348316 1 37 2 128181325 PROC NM_000312 Body chr2: 128180294-128181381 Island cg16349612 1 37 7 50849723 GRB10 NM_001001555 5′UTR chr7: 50849752-50850871 N_Shore cg16355305 1 37 12 65220152 chr12: 65218245-65219143 S_Shore cg16404784 1 37 14 38087605 chr14: 38091469-38092176 N_Shelf cg16410115 2 37 1 24240000 CNR2 NM_001841 TSS200 cg16410115 1 37 1 24240000 CNR2 NM_001841 TSS200 cg16459519 1 37 10 46970584 SYT15; SYT15; NM_031912; NM_181519; 1stExon; 5′UTR; chr10: 46969991-46971557 Island SYT15; SYT15 NM_031912; NM_181519 5′UTR; 1stExon cg16481280 1 37 6 32120955 PPT2; PRRT1; NM_005155; NM_030651; TSS1500; TSS1500; chr6: 32121829-32122529 N_Shore PPT2 NM_138717 TSS1500 cg16506566 1 37 5 10420680 43530 NM_005885 Body cg16517838 1 37 14 106154914 chr14: 106153128-106153364 S_Shore cg16542426 1 37 15 23205622 WHAMML1 NR_003521 Body chr15: 23207949-23208796 N_Shelf cg16573957 1 37 8 21970273 chr8: 21966485-21967329 S_Shelf cg16619071 1 37 19 52408324 ZNF649 NM_023074 TSS200 cg16626809 1 37 21 46825856 COL18A1 NM_130445 Body chr21: 46824531-46826234 Island cg16668042 1 37 5 132388215 HSPA4 NM_002154 Body chr5: 132387100-132388369 Island cg16668042 1 37 5 132388215 HSPA4 NM_002154 Body chr5: 132387100-132388369 Island cg16681830 1 37 20 62586920 UCKL1AS; UCKL1 NR_027287; NM_017859 Body; Body chr20: 62586919-62588218 Island cg16707641 1 37 2 175436630 WIPF1; WIPF1 NM_003387; NM_001077269 Body; Body cg16730825 1 37 11 928439 AP2A2 NM_012305 Body chr11: 925183-926083 S_Shelf cg16788797 1 37 8 75132833 cg16790849 5 37 6 31829511 NEU1 NM_000434 Body chr6: 31830299-31830948 N_Shore cg16790849 3 37 6 31829511 NEU1 NM_000434 Body chr6: 31830299-31830948 N_Shore cg16837441 1 37 20 43935222 MATN4; MATN4; NM_003833; NM_030592; 5′UTR; 5′UTR; chr20: 43935199-43935633 Island MATN4; RBPJL NM_030590; NM_014276 5′UTR; TSS1500 cg16872520 1 37 11 72929124 P2RY2; P2RY2; NM_176071; NM_176072; TSS1500; TSS1500; chr11: 72928982-72929885 Island P2RY2 NM_002564 TSS1500 cg17001464 1 37 7 130679521 FLJ43663; FLJ43663 NR_015431; NR_024153 Body; Body cg17010112 1 37 4 77227123 STBD1 NM_003943 TSS1500 chr4: 77227354-77228482 N_Shore cg17038667 1 37 11 69632883 FGF3 NM_005247 Body chr11: 69632033-69634710 Island cg17049418 1 37 6 3722453 cg17278466 2 37 17 76798203 USP36 NM_025090 Body chr17: 76798154-76798461 Island cg17310773 4 37 22 41215357 SLC25A17; SLC25A17 NM_006358; NM_006358 1stExon; 5′UTR chr22: 41215135-41215576 Island cg17310773 1 37 22 41215357 SLC25A17; SLC25A17 NM_006358; NM_006358 1stExon; 5′UTR chr22: 41215135-41215576 Island cg17319849 1 37 1 155214564 GBA; GBA; NM_001005749; NM_001005750; TSS200; TSS200; GBA; GBA NM_001005742; NM_001005741 TSS200; TSS200 cg17330305 1 37 17 56834361 PPM1E NM_014906 Body chr17: 56832961-56833986 S_Shore cg17330305 2 37 17 56834361 PPM1E NM_014906 Body chr17: 56832961-56833986 S_Shore cg17351882 1 37 17 4692162 GLTPD2 NM_001014985 TSS200 chr17: 4692249-4693977 N_Shore cg17392018 1 37 7 134590119 CALD1; CALD1; NM_033139; NM_033157; Body; Body; CALD1; CALD1; NM_033140; NM_033138; Body; Body; CALD1 NM_004342 Body cg17393572 1 37 5 176326365 HK3 NM_002115 TSS200 cg17419597 1 37 1 156211529 BGLAP NM_199173 TSS1500 chr1: 156215368-156215899 N_Shelf cg17514665 1 37 17 1657533 SERPINF2; SERPINF2; NM_000934; NM_001165921; Body; Body; chr17: 1657447-1657677 Island SERPINF2 NM_001165920 Body cg17599471 1 37 1 25174745 chr1: 25174560-25175367 Island cg17656474 1 37 12 176424 IQSEC3 NM_001170738 1stExon chr12: 175666-176400 S_Shore cg17690515 2 37 19 1360278 MUM1; MUM1 NR_024247; NM_032853 Body; Body chr19: 1360038-1360347 Island cg17745251 11 37 10 21806139 C10orf140 NM_207371 Body chr10: 21805879-21806630 Island cg17745251 7 37 10 21806139 C10orf140 NM_207371 Body chr10: 21805879-21806630 Island cg17747332 1 37 19 11071239 SMARCA4; SMARCA4; NM_003072; NM_001128849; TSS1500; TSS1500; chr19: 11071116-11072340 Island SMARCA4 NM_001128844 TSS1500 cg17749356 1 37 2 118692673 CCDC93 NM_019044 Body cg17775382 1 37 5 1584233 SDHAP3 NR_003263 Body cg17782025 1 37 3 23958698 NKIRAS1; RPL15 NM_020345; NM_002948 TSS200; 5′UTR chr3: 23957941-23959181 Island cg17794241 1 37 15 74658653 CYP11A1; CYP11A1 NM_000781; NM_001099773 Body; TSS200 chr15: 74658038-74658574 S_Shore cg17815035 1 37 18 54790380 chr18: 54788959-54789194 S_Shore cg17877237 2 37 13 32497491 EEF1DP3 NR_027062 Body cg17892069 2 37 7 70061616 AUTS2; AUTS2 NM_015570; NM_001127231 Body; Body chr7: 70060834-70061456 S_Shore cg17892069 3 37 7 70061616 ALTS2; AUTS2 NM_015570; NM_001127231 Body; Body chr7: 70060834-70061456 S_Shore cg17897445 1 37 8 7537473 chr8: 7537626-7538267 N_Shore cg17918201 1 37 10 27150106 ABI1; ABI1; NM_005470; NM_001012752; TSS200; TSS200; chr10: 27149166-27150229 Island ABI1; ABI1 NM_001012751; NM_001012750 TSS200; TSS200 cg17956079 10 37 11 73358572 PLEKHB1; PLEKHB1; NM_001130035; NM_001130036; TSS200; TSS1500; PLEKHB1; PLEKHB1; NM_001130034; NM_001130033; TSS200; Body; PLEKHB1 NM_021200 Body cg17956079 4 37 11 73358572 PLEKHB1; PLEKHB1; NM_001130035; NM_001130G36; TSS200; TSS1500; PLEKHB1; PLEKHB1; NM_001130034; NM_001130033; TSS200; Body; PLEKHB1 NM_021200 Body cg17987505 1 37 5 179246106 SQSTM1; SQSTM1 NM_001142298; NM_001142299 5′UTR; 5′UTR chr5: 179247784-179248711 N_Shore cg18007959 1 37 5 153863525 chr5: 153862142-153862451 S_Shore cg18056133 1 37 11 60609408 CCDC86 NM_024098 TSS200 chr11: 60609392-60609786 Island cg18099523 1 37 6 146285676 SHPRH; SHPRH NM_173082; NM_001042683 TSS1500; TSS1500 chr6: 146284795-146285701 Island cg18111500 3 37 14 61655727 cg18111500 10 37 14 61655727 cg18193219 1 37 3 53164697 RFT1 NM_052859 TSS1500 chr3: 53164206-53164698 Island cg18207011 1 37 14 68861095 RAD51L1; RAD51L1; NM_133509; NM_002877; Body; Body; RAD51L1 NM_133510 Body cg18217175 2 37 1 18967020 PAX7; PAX7; NM_013945; NM_002584; Body; Body; chr1: 18967251-18968119 N_Shore PAX7 NM_001135254 Body cg18217175 1 37 1 18967020 PAX7; PAX7; NM_013945; NM_002584; Body; Body; chr1: 18967251-18968119 N_Shore PAX7 NM_001135254 Body cg18220799 1 37 18 44099340 LOXHD1; LOXHD1; NM_001145473; NM_144612; TSS1500; Body; LOXHD1 NM_001145472 Body cg18239858 1 37 7 101712363 CUX1; CUX1; NM_181500; NM_181552; Body; Body; CUX1 NM_001913 Body cg18325160 1 37 3 193311041 OPA1; OPA1; NM_130836; NM_130831; 5′UTR; 5′UTR; chr3: 193310824-193311188 Island OPA1; OPA1; NM_130837; NM_130834; 5′UTR; 1stExon; OPA1; OPA1; NM_130832; NM_130836; 5′UTR; 1stExon; OPA1; OPA1; NM_130833; NM_130831; 5′UTR; 1stExon; OPA1; OPA1; NM_130837; NM_130832; 1stExon; 1stExon; OPA1; OPA1; NM_015560; NM_130835; 5′UTR; 1stExon; OPA1; OPA1; NM_130834; NM_130833; 5′UTR; 1stExon; OPA1; OPA1 NM_130835; NM_015560 5′UTR; 1stExon cg18337963 1 37 11 46383209 DGKZ; DGKZ; NM_001105540; NM_201533; 1stExon; Body; DGKZ; DGKZ; NM_001105540; NM_003646; 5′UTR; Body; DGKZ NM_201532 Body cg18391209 1 37 1 223747670 CAPN8 NM_001143962 Body chr1: 223741965-223744525 S_Shelf cg18415822 1 37 7 155857781 chr7: 155856030-155856349 S_Shore cg18452149 1 37 3 108308268 KIAA1524; DZIP3; NM_020890; NM_014648; 5′UTR; TSS200; chr3: 108308227-108308604 Island KIAA1524 NM_020890 1stExon cg18460938 1 37 15 86842630 AGBL1 NM_152336 Body cg18496140 1 37 11 44286375 ALX4 NM_021926 3′UTR cg18501555 1 37 4 111554966 PITX2; PITX2 NM_153427; NM_153426 5′UTR; 5′UTR chr4: 111554965-111555504 Island cg18561676 2 37 1 148855262 chr1: 148853996-148855761 Island cg18561676 4 37 1 148855262 chr1: 148853996-148855761 Island cg18580296 1 37 7 15726411 MEOX2 NM_005924 TSS200 cg18580296 2 37 7 15726411 MEOX2 NM_005924 TSS200 cg18633379 1 37 18 59855274 PIGN; PIGN; NM_012327; NM_176787; TSS1500; TSS1500; chr18: 59853977-59855252 S_Shore KIAA1468 NM_020854 Body cg18633561 1 37 7 121943354 FEZF1; FEZF1 NM_001160264; NM_001024613 Body; Body chr7: 121943867-121944538 N_Shore cg18676488 1 37 5 70848105 BDP1 NM_018429 Body cg18676488 2 37 5 70848105 BDP1 NM_018429 Body cg18686165 1 37 3 57200492 IL17RD NM_017563 TSS1500 chr3: 57198243-57199378 S_Shore cg18700813 3 37 14 102702123 RAGE NM_014226 Body cg18710412 1 37 5 90654191 cg18724069 1 37 5 39721760 chr5: 39721548-39721835 Island cg18762036 1 37 2 107872062 cg18779296 1 37 4 41878119 chr4: 41880224-41880500 N_Shelf cg18855674 1 37 8 72469553 chr8: 72468560-72469561 Island cg18862888 4 37 10 31346162 cg18902057 1 37 16 88636444 ZC3H18 NM_144604 TSS1500 chr16: 88636176-88637333 Island cg18927185 1 37 6 33091634 HLA-DPB2 NR_001435 Body cg18954388 1 37 11 20621495 SLC6A5 NM_004211 Body chr11: 20622720-20623399 N_Shore cg19037304 2 37 7 19812760 TMEM196 NM_152774 TSS1500 chr7: 19812569-19813005 Island cg19132477 1 37 3 8484313 cg19132477 1 37 3 8484313 cg19154754 1 37 11 48977527 cg19157696 1 37 11 27384984 CCDC34; CCDC34 NM_080654; NM_030771 TSS200; TSS200 chr11: 27384359-27384870 S_Shore cg19190016 1 37 17 81025684 chr17: 81024122-81024360 S_Shore cg19207486 1 37 19 22323107 chr19: 22320743-22320976 S_Shelf cg19227053 1 37 20 60116795 CDH4 NM_001794 Body chr20: 60119507-60119712 N_Shelf cg19265948 2 37 12 23229286 cg19265948 1 37 12 23229286 cg19327615 1 37 20 19955436 RIN2 NM_018993 Body chr20: 19955536-19956034 N_Shore cg19327615 1 37 20 19955436 RIN2 NM_018993 Body chr20: 19955536-19956034 N_Shore cg19380675 1 37 22 32808489 C22orf28 NM_014306 TSS1500 chr22: 32807825-32808285 S_Shore cg19409687 1 37 11 65682960 chr11: 65685100-65685364 N_Shelf cg19441646 1 37 14 102695456 RAGE NM_014226 3′UTR chr14: 102695455-102695804 Island cg19448318 2 37 6 30698784 FLOT1 NM_005803 Body cg19469087 1 37 7 98556941 TRRAP NM_003496 Body chr7: 98552746-98552962 S_Shelf cg19480274 1 37 20 37098327 chr20: 37101171-37101742 N_Shelf cg19484381 1 37 6 28890673 TRIM27 NM_006510 Body chr6: 28890951-28892013 N_Shore cg19488906 1 37 6 161694840 AGPAT4 NM_020133 5′UTR cg19513744 2 37 3 56836209 ARHGEF3; ARHGEF3 NM_001128615; NM_019555 Body; TSS1500 chr3: 56835650-56836210 Island cg19514542 1 37 10 125614284 CPXM2 NM_198148 Body chr10: 125617057-125617329 N_Shelf cg19559392 7 37 2 39103372 MORN2; DHX57 NM_001145450; NM_198963 5′UTR; TSS1500 chr2: 39102805-39103214 S_Shore cg19562312 1 37 10 44069847 ZNF239; ZNF239; NM_001099284; NM_001099282; 5′UTR; 5′UTR; chr10: 44069359-44070179 Island ZNF239 NM_001099283 5′UTR cg19625088 1 37 5 87976156 LOC645323 NR_015436 Body chr5: 87976094-87976546 Island cg19627869 1 37 12 56391069 SUOX; SUOX; NM_001032386; NM_001032387; 5′UTR; 1stExon; SUOX; SUOX; NM_001032386; NM_001032387; 1stExon; 5′UTR; SUOX; SUOX NM_000456; NM_000456 5′UTR; 1stExon cg19693446 1 37 14 102144192 cg19749898 1 37 11 1712765 HCCA2 NM_053005 Body chr11: 1715347-1715607 N_Shelf cg19777001 1 37 14 103150180 RCOR1 NM_015156 Body cg19837938 1 37 5 23507458 PRDM9 NM_020227 TSS1500 cg19837938 2 37 5 23507458 PRDM9 NM_020227 TSS1500 cg19852211 1 37 5 140187240 PCDHA2; PCDHA1; NM_018905; NM_031411; Body; Body; chr5: 140186792-140187268 Island PCDHA1; PCDHA4; NM_018900; NM_018907; Body; 1stExon; PCDHA3; PCDHA4 NM_018906; NM_031500 Body; 1stExon cg19852211 1 37 5 140187240 PCDHA2; PCDHA1; NM_018905; NM_031411; Body; Body; chr5: 140186792-140187268 Island PCDHA1; PCDHA4; NM_018900; NM_018907; Body; 1stExon; PCDHA3; PCDHA4 NM_018906; NM_031500 Body; 1stExon cg19855573 2 37 1 152297873 FLG NM_002016 TSS200 cg19865375 1 37 7 86629801 KIAA1324L; KIAA1324L NM_001142749; NR030672 Body; Body cg19875976 1 37 9 114246783 KIAA0368 NM_001080398 Body chr9: 114245044-114246784 Island cg19875976 1 37 9 114246783 KIAA0368 NM_001080398 Body chr9: 114245044-114246784 Island cg19991948 1 37 10 121335173 TIAL1; TIAL1 NM_001033925; NM_003252 3′UTR; 3′UTR cg19998654 1 37 2 37458983 CEBPZ; C2orf56; NM_005760; NM_144736; TSS1500; Body; chr2: 37458398-37459199 Island C2orf56 NM_001083946 Body cg20059151 1 37 1 95286311 SLC44A3; SLC44A3 NM_152369; NM_001114106 5′UTR; Body chr1: 95285602-95286319 Island cg20069765 1 37 6 33036464 HLA-DPA1 NM_033554 Body cg20081364 1 37 20 13202225 ISM1 NM_080826 TSS200 chr20: 13200670-13202616 Island cg20155875 1 37 17 66452567 WIPI1 NM_017983 Body chr17: 66453349-66454137 N_Shore cg20162076 3 37 6 6588089 LY86; LOC285780 NM_004271; NR_026970 TSS1500; Body cg20162076 5 37 6 6588089 LY86; LOC285780 NM_004271; NR_026970 TSS1500; Body cg20172795 1 37 6 127441199 RSPO3 NM_032784 Body chr6: 127441553-127441760 N_Shore cg20183094 4 37 7 121950924 chr7: 121950249-121950927 Island cg20200361 6 37 2 43775888 THADA; THADA NM_022065; NM_001083953 Body; Body cg20268522 2 37 11 112832152 NCAM1; NCAM1; NM_001076682; NM_001076682; 1stExon; 5′UTR; NCAM1; NCAM1; NM_000615; NM_181351; 5′UTR; 1stExon; NCAM1; NCAM1 NM_181351; NM_000615 5′UTR; 1stExon cg20274430 1 37 22 41075992 MCHR1 NM_005297 Body cg20294319 1 37 13 47253842 LRCH1; LRCH1; NM_015116; NM_001164213; Body; Body; LRCH1 NM_001164211 Body cg20319405 1 37 11 10830230 EIF4G2; EIF4G2 NM_001418; NM_001042559 5′UTR; 5′UTR chr11: 10829361-10831121 Island cg20327784 1 37 17 73703307 SAP30BP NM_013260 3′UTR cg20327784 1 37 17 73703307 SAP30BP NM_013260 3′UTR cg20458353 2 37 7 21260293 cg20500836 1 37 17 78818645 RPTOR; RPTOR NM_001163034; NM_020761 Body; Body chr17: 78818440-78818696 Island cg20532937 1 37 10 13748985 FRMD4A NM_018027 Body cg20555922 1 37 20 33880266 FAM83C NM_178468 TSS200 chr20: 33879904-33880215 S_Shore cg20587808 1 37 3 184320123 chr3: 184320005-184320218 Island cg20593868 1 37 20 62588672 UCKL1; ZNF512B NM_017859; NM_020713 TSS1500; 3′UTR chr20: 62586919-62588218 S_Shore cg20593868 1 37 20 62588672 UCKL1; ZNF512B NM_017859; NM_020713 TSS1500; 3′UTR chr20: 62586919-62588218 S_Shore cg20684251 3 37 19 51840554 VSIG10L NM_001163922 Body chr19: 51842128-51842353 N_Shore cg20684251 1 37 19 51840554 VSIG10L NM_001163922 Body chr19: 51842128-51842353 N_Shore cg20707630 1 37 15 25018449 chr15: 25018174-25018533 Island cg20743744 1 37 4 1243849 C4orf42; CTBP1; NM_052861; NM_001328; TSS1500; TSS1500; chr4: 1241412-1244111 Island CTBP1 NM_001012614 TSS1500 cg20888142 1 37 3 12045662 SYN2; SYN2 NM_003178; NM_133625 TSS200; TSS200 chr3: 12045652-12046627 Island cg20914725 1 37 2 74776831 LOXL3 NM_032603 Body chr2: 74776016-74776897 Island cg21000072 1 37 1 3567408 WDR8 NM_017818 TSS1500 chr1: 3566445-3569636 Island cg21007262 1 37 20 18122863 PET117; CSRP2BP NM_001164811; NM_020536 Body; TSS200 chr20: 18117962-18118989 S_Shelf cg21102950 4 37 3 155524173 C3orf33 NM_173657 TSS200 chr3: 155523740-155524174 Island cg21117978 1 37 2 64957132 cg21200923 1 37 18 9481257 RALBP1 NM_006788 5′UTR chr18: 9478452-9478920 S_Shelf cg21211367 1 37 2 162094118 chr2: 162094460-162096195 N_Shore cg21231400 2 37 5 155108085 chr5: 155107504-155108934 Island cg21234471 2 37 9 92023797 SEMA4D; SEMA4D NM_001142287; NM_006378 5′UTR; 5′UTR cg21242508 1 37 22 28199621 chr22: 28192793-28198592 S_Shore cg21251791 1 37 2 3129858 cg21263471 1 37 17 56399584 BZRAP1; BZRAP1 NM_004758; NM_024418 Body; Body chr17: 56401728-56402343 N_Shelf cg21314304 1 37 17 41135517 RUNDC1 NM_173079 Body chr17: 41132462-41133367 S_Shelf cg21434114 1 37 18 3450282 TGIF1; TGIF1; NM_174886; NM_173208; 5′UTR; 5′UTR; chr18: 3448006-3452360 Island TGIF1; TGIF1; NM_003244; NM_173209; 5′UTR; 5′UTR; TGIF1; TGIF1; NM_170695; NM_173210; TSS1500; TSS1500; TGIF1; TGIF1 NM_003244; NM_173207 1stExon; Body cg21441716 1 37 1 176317762 cg21450738 1 37 8 100909366 chr8: 100905657-100906003 S_Shelf cg21481322 1 37 8 40984072 cg21503582 1 37 7 151001017 chr7: 151000579-151001042 Island cg21503582 1 37 7 151001017 chr7: 151000579-151001042 Island cg21549195 1 37 19 52452368 chr19: 52452316-52452543 Island cg21552319 1 37 6 24356996 DCDC2; KAAG1 NM_016356; NM_181337 Body; TSS200 chr6: 24357719-24358309 N_Shore cg21552319 2 37 6 24356996 DCDC2; KAAG1 NM_016356; NM_181337 Body; TSS200 chr6: 24357719-24358309 N_Shore cg21584710 1 37 17 72306141 DNAI2 NM_023036 Body cg21584983 1 37 19 11640070 ECSIT; ECSIT; NM_001142464; NR_024551; TSS200; TSS1500; chr19: 11639614-11639897 S_Shore ECSIT; ECSIT NM_001142465; NM_016581 TSS200; TSS200 cg21584983 1 37 19 11640070 ECSIT; ECSIT; NM_001142464; NR_024551; TSS200; TSS1500; chr19: 11639614-11639897 S_Shore ECSIT; ECSIT NM_001142465; NM_016581 TSS200; TSS200 cg21590497 1 37 19 23299649 chr19: 23299727-23300167 N_Shore cg21593588 1 37 4 109574236 OSTC NM_021227 Body chr4: 109571693-109572039 S_Shelf cg21643086 15 37 6 27243037 cg21643086 12 37 6 27243037 cg21686797 1 37 6 30303645 TRIM39; TRIM39 NM_172016; NM_021253 Body; Body cg21715599 1 37 15 92463554 SLCO3A1; SLCO3A1 NM_001145044; NM_013272 Body; Body chr15: 92459266-92459678 S_Shelf cg21729798 1 37 6 24357078 DCDC2; KAAG1 NM_016356; NM_181337 Body; TSS200 chr6: 24357719-24358309 N_Shore cg21737039 1 37 4 8271391 HTRA3 NM_053044 TSS200 chr4: 8271214-8272091 Island cg21737039 2 37 4 8271391 HTRA3 NM_053044 TSS200 chr4: 8271214-8272091 Island cg21857885 3 37 14 60337864 RTN1 NM_021136 TSS1500 chr14: 60336951-60337461 S_Shore cg21857885 2 37 14 60337864 RTN1 NM_021136 TSS1500 chr14: 60336951-60337461 S_Shore cg21947488 2 37 16 2185289 PKD1; PKD1 NM_001009944; NM_000296 Body; Body chr16: 2185139-2186406 Island cg21947488 2 37 16 2185289 PKD1; PKD1 NM_001009944; NM_000296 Body; Body chr16: 2185139-2186406 Island cg22028161 1 37 2 95658954 cg22078976 1 37 20 58515561 C20orf177; C20orf177; NM_022106; NM_022106; 1stExon; 5′UTR; chr20: 58514071-58515636 Island PPP1R3D NM_006242 TSS1500 cg22079902 1 37 5 23507644 PRDM9 NM_020227 TSS200 cg22169384 2 37 12 129417623 GLT1D1 NM_144669 Body cg22199410 1 37 12 51985016 SCN8A NM_014191 TSS200 chr12: 51984474-51985284 Island cg22205573 4 37 13 113968561 LAMP1 NM_005561 Body cg22205573 1 37 13 113968561 LAMP1 NM_005561 Body cg22240520 1 37 7 158855297 VIPR2 NM_003382 Body chr7: 158856817-158857209 N_Shore cg22380533 1 37 19 55690741 SYT5 NM_003180 5′UTR chr19: 55690182-55691623 Island cg22384904 1 37 1 227975220 chr1: 227975295-227976570 N_Shore cg22389137 1 37 4 113432227 chr4: 113431825-113432596 Island cg22491379 2 37 2 120553625 PTPN4 NM_002830 5′UTR cg22491379 1 37 2 120553625 PTPN4 NM_002830 5′UTR cg22499893 1 37 1 24307535 SFRS13A; SFRS13A NM_054016; NM_006625 TSS1500; TSS1500 chr1: 24306363-24307017 S_Shore cg22510362 1 37 16 87251839 chr16: 87251634-87251840 Island cg22630628 1 37 10 73337125 CDH23; CDH23 NM_052836; NM_022124 Body; Body cg22657457 1 37 5 75469969 SV2C NM_014979 Body chr5: 75469968-75470173 Island cg22730967 1 37 1 203097454 ADORA1; ADORA1 NM_001048230; NM_000674 5′UTR; 5′UTR chr1: 203097233-203097496 Island cg22730967 1 37 1 203097454 ADORA1; ADORA1 NM_001048230; NM_000674 5′UTR; 5′UTR chr1: 203097233-203097496 Island cg22791936 1 37 6 137243410 SLC35D3; SLC35D3 NM_001008783; NM_001008783 1stExon; 5′UTR chr6: 137242315-137245442 Island cg22819135 1 37 5 41920822 C5orf51 NM_075921 3′UTR cg22821289 1 37 11 115581830 cg22827060 1 37 13 30424359 UBL3; UBL3 NM_007106; NM_007106 1stExon; 5′UTR chr13: 30423921-30424941 Island cg22836434 1 37 11 86014570 C11orf73; C11orf73; NM_016401; NR_024597; Body; Body; C11orf73; C11orf73 NR_024596; NR_024598 Body; Body cg22856949 1 37 10 127408044 C10orf137 NM_015608 TSS200 chr10: 127407627-127408566 Island cg22877380 1 37 2 131804299 ARHGEF4; ARHGEF4 NM_032995; NM_015320 3′UTR; 3′UTR cg22963777 1 37 20 34115350 C20orf173; C20orf173 NM_001145350; NR026933 3′UTR; Body cg23013894 1 37 5 5025912 cg23067355 1 37 6 125425012 chr6: 125420743-125421141 S_Shelf cg23078194 1 37 6 27661566 cg23146197 1 37 12 66271002 HMGA2; HMGA2 NM_003484; NM_003483 Body; Body cg23191118 1 37 8 145560718 SCRT1 NM_031309 TSS1500 chr8: 145555342-145562310 Island cg23210118 1 37 10 95653378 TMEM20; TMEM20 NM_153226; NM_001134658 TSS1500; TSS1500 chr10: 95653641-95654181 N_Shore cg23226134 5 37 1 11866389 CLCN6; CLCN6; NM_001286; NM_021737; 1stExon; 1stExon; chr1: 11865462-11866566 Island CLCN6; CLCN6; NM_021735; NM_021736; 1stExon; 1stExon; MTHFR NM_005957 TSS1500 cg23232056 1 37 1 121461578 cg23239690 3 37 10 131505815 MGMT NM_002412 Body cg23239690 1 37 10 131505815 MGMT NM_002412 Body cg23275972 1 37 7 157224017 cg23283362 1 37 1 45263371 chr1: 45265534-45266783 N_Shelf cg23285761 2 37 8 38089462 DDHD2; DDHD2; NM_015214; NM_001164234; 5′UTR; 5′UTR; chr8: 38088735-38089956 Island DDHD2 NM_001164232 TSS200 cg23350744 1 37 5 122422098 chr5: 122424337-122424539 N_Shelf cg23369529 1 37 1 68149989 GADD45A NM_001924 TSS1500 chr1: 68150913-68152270 N_Shore cg23442853 1 37 3 122296488 PARP15; PARP15 NM_001113523; NM_001113523 5′UTR; 1stExon chr3: 122296612-122296828 N_Shore cg23465289 1 37 5 54909384 cg23509665 2 37 7 158293697 PTPRN2; PTPRN2; NM_002847; NM_130842; Body; Body; PTPRN2 NM_130843 Body cg23517116 1 37 8 65499841 chr8: 65499748-65500145 Island cg23574427 1 37 4 122746245 BBS7; CCNA2 NM_176824; NM_001237 3′UTR; TSS1500 chr4: 122744557-122745267 S_Shore cg23645639 1 37 19 21203403 ZNF430 NM_025189 TSS200 cg23660155 1 37 1 22915626 EPHA8; EPHA8 NM_001006943; NM_020526 Body; Body cg23692620 1 37 19 19971862 chr19: 19971577-19971863 Island cg23730260 1 37 11 8290409 chr11: 8289532-8290322 S_Shore cg23777173 2 37 12 132698353 GALNT9 NM_001122636 Body chr12: 132696661-132697724 S_Shore cg23802518 1 37 10 80827482 ZMIZ1; LOC283050; NM_020338; NR024431; TSS1500; TSS1500; chr10: 80827070-80830537 Island LOC283050; LOC283050 NR024429; NR015429 TSS1500; TSS1500 cg23813156 1 37 20 47935243 chr20: 47934839-47935684 Island cg23837438 1 37 10 135132457 chr10: 135132006-135132458 Island cg23951961 1 37 4 42154912 BEND4; BEND4 NM_207406; NM_001159547 TSS200; TSS200 chr4: 42152766-42154984 Island cg23970785 1 37 16 11036526 DEXI NM_014015 TSS1500 chr16: 11035496-11036696 Island cg24030735 1 37 17 10533089 MYH3 NM_002470 Body cg24099067 1 37 6 26758750 cg24177983 1 37 11 2398403 CD81 NM_004356 TSS200 chr11: 2398223-2399598 Island cg24216966 1 37 6 31540121 LTA; LTA; NM_000595; NM_001159740; 1stExon; 5′UTR; LTA NM_000595 5′UTR cg24243790 1 37 4 9760736 cg24285811 1 37 9 139143869 chr9: 139143508-139144429 Island cg24300033 1 37 2 241640149 chr2: 241640409-241641359 N_Shore cg24330818 1 37 13 33002388 N4BP2L1; N4BP2L1 NM_052818; NM_001079691 TSS200; TSS200 chr13: 33001249-33002078 S_Shore cg24364491 2 37 6 32806906 TAP2; TAP2 NM_018833; NM_000544 TSS1500; TSS1500 chr6: 32806284-32806669 S_Shore cg24408706 2 37 11 363484 cg24453123 1 37 15 35374148 cg24453123 1 37 15 35374148 cg24533904 1 37 1 184467193 C1orf21 NM_030806 Body cg24541871 1 37 2 55845713 SMEK2; SMEK2 NM_001122964; NM_020463 TSS1500; TSS1500 chr2: 55844267-55845065 S_Shore cg24547359 1 37 1 53975500 GLIS1 NM_147193 Body cg24550933 1 37 1 111932556 LOC441897 NR_029429 TSS200 cg24563317 1 37 8 48872822 MCM4; MCM4; NM_005914; NM_182746; TSS1500; TSS1500; chr8: 48872458-48873907 Island PRKDC; PRKDC NM_006904; NM_001081640 TSS200; TSS200 cg24594224 1 37 6 33136015 COL11A2; COL11A2; NM_080679; NM_080681; Body; Body; COL11A2 NM_080680 Body cg24629356 1 37 1 35122551 cg24706188 1 37 8 55088456 cg24710435 1 37 10 14543847 cg24734300 1 37 7 35677335 HERPUD2 NM_022373 Body cg24766104 1 37 19 16309072 AP1M1; AP1M1 NM_032493; NM_001130524 Body; Body chr19: 16308557-16309313 Island cg24766104 2 37 19 16309072 AP1M1; AP1M1 NM_032493; NM_001130524 Body; Body chr19: 16308557-16309313 Island cg24779831 1 37 2 2799370 cg24794433 1 37 9 124462172 DAB2IP NM_032552 Body chr9: 124461797-124462190 Island cg24811352 1 37 5 140529499 PCDHB6 NM_018939 TSS1500 chr5: 140531157-140532017 N_Shore cg24839562 1 37 6 31673423 LY6G6F NM_001003693 TSS1500 chr6: 31670594-31671274 S_Shelf cg24856050 1 37 19 3192433 NCLN NM_020170 Body chr19: 3192416-3192705 Island cg24864663 1 37 15 43532243 TGM5; TGM5 NM_201631; NM_004245 Body; Body cg24891539 3 37 8 55370407 SOX17 NM_022454 TSS200 chr8: 55370170-55372525 Island cg24891539 1 37 8 55370407 SOX17 NM_022454 TSS200 chr8: 55370170-55372525 Island cg24917945 1 37 10 120514927 C10orf46 NM_153810 TSS200 chr10: 120513949-120515108 Island cg24968786 1 37 11 66360800 CCDC87; CCS NM_018219; NM_005125 TSS1500; Body chr11: 66360097-66360834 Island cg25013910 1 37 2 1478219 TPO; TPO; NM_175719; NM_000547; Body; Body; chr2: 1480758-1481631 N_Shelf TPO; TPO NM_175721; NM_175722 Body; Body cg25025455 1 37 3 134204912 CEP63; CEP63; NM_001042383; NM_001042400; 5′UTR; 5′UTR; chr3: 134204520-134205439 Island ANAPC13; CEP63; NR_024400; NM_001042384; TSS200; 5′UTR; CEP63; ANAPC13; NM_025180; NM_015391; TSS200; TSS200; CEP63; ANAPC13 NM_001042400; NR_024401 1stExon; TSS200 cg25092989 1 37 8 10932494 XKR6 NM_173683 Body chr8: 10928984-10929211 S_Shelf cg25100962 2 37 12 31782808 cg25124476 1 37 7 150497738 TMEM176B; TMEM176B; NM_001101312; NM_001101314; TSS200; TSS200; chr7: 150496809-150498206 Island TMEM176A; TMEM176B; NM_018487; NM_014020; TSS200; 5′UTR; TMEM176B NM_001101311 TSS200 cg25149069 2 37 1 233464229 KIAA1804 NM_032435 1stExon chr1: 233463526-233464414 Island cg25154733 2 37 13 28965632 FLT1; FLT1; NM_001159920; NM_001160030; Body; Body; FLT1 NM_002019 Body cg25161386 1 37 17 27621177 NUFIP2 NM_020772 TSS200 chr17: 27621169-27621455 Island cg25181381 1 37 11 134373655 cg25193384 1 37 7 39837692 chr7: 39833494-39833725 S_Shelf cg25194328 1 37 5 54472477 chr5: 54468783-54469324 S_Shelf cg25206705 2 37 17 1082774 ABR; ABR NM_021962; NM_001159746 Body; 5′UTR chr17: 1082376-1083833 Island cg25236028 1 37 17 767334 NXN NM_022463 Body cg25246158 1 37 19 1940184 CSNK1G2 NM_001319 TSS1500 chr19: 1940303-1941940 N_Shore cg25259296 1 37 21 43235862 PRDM15; PRDM15 NM_022115; NM_001040424 Body; Body chr21: 43236025-43236510 N_Shore cg25328184 1 37 5 110406414 TSLP NM_033035 TSS1500 chr5: 110408704-110409039 N_Shelf cg25328184 1 37 5 110406414 TSLP NM_033035 TSS1500 chr5: 110408704-110409039 N_Shelf cg25334660 1 37 8 42270520 chr8: 42268436-42268759 S_Shore cg25356214 2 37 12 51611871 POU6F1 NR_026893 TSS1500 chr12: 51610892-51611724 S_Shore cg25367905 1 37 5 176790350 RGS14 NM_006480 Body chr5: 176789978-176790296 S_Shore cg25370231 1 37 10 13391182 SEPHS1 NM_012247 TSS1500 cg25402787 1 37 15 53084679 chr15: 53086629-53086858 N_Shore cg25409448 2 37 19 49558849 CGB7; CGB7 NM_033142; NM_033142 5′UTR; 1stExon chr19: 49559222-49560497 N_Shore cg25417551 1 37 17 35767582 TADA2A; TADA2A; NM_001488; NM_133439; 1stExon; 1stExon; chr17: 35766664-35767335 S_Shore ACACA; TADA2A; NM_198834; NM_001166105; TSS1500; 5′UTR; ACACA; TADA2A; NM_198839; NM_001488; TSS1500; 5′UTR; TADA2A NM_133439 5′UTR cg25427880 1 37 10 102322128 chr10: 102321832-102322395 Island cg25456593 1 37 11 70672858 SHANK2 NM_012309 Body chr11: 70672834-70673055 Island cg25502179 1 37 3 46875342 PRSS42 NM_182702 Body chr3: 46874892-46875769 Island cg25545088 1 37 6 43398446 ABCC10 NM_033450 TSS1500 chr6: 43395188-43395894 S_Shelf cg25550629 1 37 12 53546895 cg25714381 1 37 7 76751893 CCDC146 NM_020879 TSS200 chr7: 76750995-76751394 S_Shore cg25734864 2 37 13 113812986 PROZ NM_003891 1stExon cg25756867 1 37 3 180042726 cg25758828 1 37 2 113976143 PAX8; PAX8; NM_013953; NM_003466; 3′UTR; Body; PAX8; PAX8; NM_013952; NM_013951; 3′UTR; Body; PAX8; LOC440839 NM_013992; NR_029399 3′UTR; Body cg25778535 1 37 11 8190572 RIC3; RIC3; NM_001135109; NM_024557; 1stExon; 5′UTR; chr11: 8190226-8190671 Island RIC3; RIC3 NM_001135109; NM_024557 5′UTR; 1stExon cg25803630 2 37 8 29885309 chr8: 29884771-29885310 Island cg25820279 1 37 2 177001909 chr2: 177001221-177001783 S_Shore cg25824218 1 37 12 25104798 chr12: 25101607-25102073 S_Shelf cg25824218 1 37 12 25104798 chr12: 25101607-25102073 S_Shelf cg25859012 1 37 2 219524278 BCS1L; ZNF142; NM_004328; NM_001105537; TSS200; TSS200; chr2: 219523901-219524577 Island BCS1L NM_001079866 TSS200 cg25884094 1 37 8 17785204 PCM1 NM_006197 5′UTR chr8: 17780032-17781272 S_Shelf cg25894839 1 37 1 161696082 FCRLB NM_001002901 Body chr1: 161695637-161697298 Island cg25943588 1 37 11 14993913 CALCA; CALCA; NM_001033952; NM_001033953; TSS200; TSS200; chr11: 14995128-14995908 N_Shore CALCA NM_001741 TSS200 cg26003814 3 37 1 16444599 cg26053864 1 37 15 35087635 ACTC1 NM_005159 5′UTR cg26074111 1 37 6 24776063 GMNN NM_015895 5′UTR chr6: 24775046-24775729 S_Shore cg26084511 1 37 7 20818226 chr7: 20817455-20818227 Island cg26091183 3 37 17 78387382 LOC100294362 NR_029376 Body chr17: 78388437-78389722 N_Shore cg26091183 2 37 17 78387382 LOC100294362 NR_029376 Body chr17: 78388437-78389722 N_Shore cg26105278 1 37 1 3624054 TP73; TP73; NM_001126240; NM_005427; Body; Body; chr1: 3623318-3623521 S_Shore TP73; TP73 NM_001126242; NM_001126241 Body; Body cg26114595 1 37 17 28395749 EFCAB5; EFCAB5; NR_026738; NM_198529; Body; Body; EFCAB5 NM_001145053 Body cg26129303 1 37 8 142095375 cg26148236 1 37 2 233497957 EFHD1; EFHD1 NM_025202; NR_027663 TSS1500; Body chr2: 233497826-233499727 Island cg26149738 1 37 19 34287125 KCTD15; KCTD15; NM_001129994; NM_024076; TSS1500; TSS1500; chr19: 34286184-34289135 Island KCTD15 NM_001129995 TSS1500 cg26163463 1 37 5 139926773 EIF4EBP3; NM_003732; NM_020690 TSS1500; Body chr5: 139927157-139927491 N_Shore ANKHD1-EIF4EBP3 cg26203055 2 37 18 19284713 ABHD3; ABHD3 NM_138340; NM_138340 1stExon; 5′UTR chr18: 19284165-19285052 Island cg26266950 2 37 7 19160621 chr7: 19156050-19158042 S_Shelf cg26384229 9 37 12 38710491 ALG10B NM_001013620 TSS200 chr12: 38710392-38710643 Island cg26384229 14 37 12 38710491 ALG10B NM_001013620 TSS200 chr12: 38710392-38710643 Island cg26490274 1 37 16 4385435 GLIS2 NM_032575 Body cg26524638 1 37 11 2481449 KCNQ1; KCNQ1 NM_181798; NM_000218 TSS1500; Body cg26541533 1 37 6 164256018 chr6: 164255450-164256062 Island cg26573704 2 37 5 33892223 ADAMTS12 NM_030955 TSS200 chr5: 33892191-33892403 Island cg26575535 1 37 16 65157839 chr16: 65154656-65157664 S_Shore cg26586710 1 37 10 134216688 PWWP2B; PWWP2B NM_001098637; NM_138499 Body; Body chr10: 134218268-134219615 N_Shore cg26588943 2 37 4 172734718 GALNTL6; GALNTL6 NM_001034845; NM_001034845 1stExon; 5′UTR chr4: 172733734-172735118 Island cg26616283 1 37 7 11871535 THSD7A NM_015204 1stExon cg26616283 1 37 7 11871535 THSD7A NM_015204 1stExon cg26634911 2 37 4 47916863 NFXL1 NM_152995 TSS1500 chr4: 47915861-47916880 Island cg26651514 1 37 13 33864734 cg26654519 1 37 8 142517494 FLJ43860 NM_207414 TSS200 cg26712605 1 37 6 37745367 cg26759552 2 37 7 139877471 LOC100134229; JHDM1D NR_024451; NM_030647 Body; TSS1500 chr7: 139875411-139877493 Island cg26777456 1 37 12 54454250 FLJ12825 NR_026655 Body chr12: 54454249-54454458 Island cg26835440 2 37 8 55037773 cg26919149 2 37 6 168501903 chr6: 168501902-168502790 Island cg26933136 1 37 1 28661842 MED18; MED18 NM_001127350; NM_017638 3′UTR; 3′UTR cg26946235 2 37 10 134890799 chr10: 134891010-134893402 N_Shore cg26994413 1 37 12 130909408 RIMBP2 NM_015347 Body chr12: 130908777-130909191 S_Shore cg27037109 1 37 19 12512034 ZNF799 NM_001080821 TSS200 chr19: 12511608-12512144 Island cg27042491 2 37 10 77191686 chr10: 77191061-77191571 S_Shore cg27062060 1 37 17 79258687 SLC38A10; SLC38A10 NM_001037984; NM_138570 Body; Body chr17: 79259282-79259537 N_Shore cg27072218 1 37 13 106912755 cg27101157 1 37 17 62340122 TEX2 NM_018469 5′UTR chr17: 62339803-62340799 Island cg27140170 1 37 2 231280096 SP100; SP100 NM_001080391; NM_003113 TSS1500; TSS1500 cg27181253 2 37 1 113051846 WNT2B; WNT2B; NM_004185; NM_024494; Body; 1stExon; chr1: 113050813-113052301 Island WNT2B NM_024494 5′UTR cg27207308 1 37 20 47935683 chr20: 47934839-47935684 Island cg27313674 1 37 20 6035120 LRRN4 NM_152611 TSS1500 chr20: 6032675-6033517 S_Shore cg27323009 1 37 5 110408974 TSLP; TSLP NM_138551; NM_033035 TSS200; Body chr5: 110408704-110409039 Island cg27343123 1 37 2 62423136 B3GNT2 NM_006577 TSS200 chr2: 62422191-62424458 Island cg27391127 1 37 10 104415919 TRIM8 NM_030912 Body chr10: 104416555-104417165 N_Shore cg27426287 1 37 10 30025782 SVIL NM_003174 TSS1500 chr10: 30024072-30026077 Island cg27445005 1 37 18 76190006 chr18: 76189718-76190190 Island cg27445005 2 37 18 76190006 chr18: 76189718-76190190 Island cg27553486 1 37 7 930964 C7orf20 NM_015949 Body chr7: 930913-931215 Island cg27633010 1 37 10 135097477 TUBGCP2 NM_006659 Body chr10: 135097516-135097801 N_Shore cg27633010 3 37 10 135097477 TUBGCP2 NM_006659 Body chr10: 135097516-135097801 N_Shore cg27640020 1 37 19 19002253 GDF1; LASS1; NM_001492; NM_198207; 5′UTR; Body; chr19: 19006031-19007546 N_Shelf LASS1 NM_021267 Body ch.16.1667936F 1 36 16 73947777 ch.2.3048096R 1 36 2 147986881

Data preprocessing. Statistical analysis was performed using R (v. 3.5.0). Raw .IDAT files were processed using the minfi package (v. 1.26.2). Illumina 850k (EPIC) array data were subset to only those sites also included in the 450k array. Preprocessing and normalization were performed using the preprocess Funnorm function. All samples passed internal controls included on each chip and had detection p≤0.01 for ≥97% of cytosine-guanosine dinucleotide (CpG) positions included on each array. Epigenome-wide association studies traditionally have used DNA methylation beta values, defined as the fraction methylation (0-1 scale) for a particular CpG site. Beta values, however, are characterized by high heteroscedasticity (most beta values fall within extreme high- and low-percent methylation levels), and questions have been raised regarding statistical validity of beta value analysis [24]. Therefore, the inventors also analyzed M values (the log₂ ratio of methylated:unmethylated probe intensities for a given CpG site), which are approximately homoscedastic. The inventors excluded from analysis CpG probes located on sex chromosomes, probes with known single nucleotide polymorphisms (SNPs) with minor allele frequency of ≥5%, and probes not detected in all samples, leaving a final n=435,118 CpG sites for analysis in each sample.

Modeling. Elastic-net regularized generalized linear models were developed using the glmnet package (v. 2.0-16). As model overfitting is a frequently-occurring problem when developing classifiers on high-dimensional data, the inventors implemented three strategies to reduce potential overfitting. First, the inventors performed 7-fold internal cross-validation during development via the cv.glmnet function, utilizing the ‘one standard error rule’ when selecting lambda values [69]. Second, the inventors tested models on lockbox data not used for training (FIG. 2). Finally, the inventors repeated the model development and testing with 40 cycles of random splits of data into development and lockbox (validation) subsets. During each cycle of development, data were first randomly split into 60% development and 40% lockbox sets. Development data were then used to generate regularized cross-validated models and these models were tested on lockbox data and performance characteristics recorded. Model performance was assessed by the mean c-statistic (area under the receiver operator characteristic curve AUC-ROC), diagnostic odds ratio, accuracy, sensitivity, and specificity. The identity of DNA methylation sites (features) selected by glmnet for inclusion in each model, and the total number of sites required by each model, were recorded and compared. The performance of models by chip type (450k vs. 850k) was assessed by comparing accuracies using Fisher's exact test of a 2×2 contingency table.

Ontology analysis. Genes associated with CpG sites selected at least once during model development (n=969) were analyzed using Ingenuity Pathway Analysis (IPA, Qiagen) v. 48207413 build 2019-06-16 using default settings.

Case and control eligibility and Selection Process.

1. Subject Inclusion:

1.1. A subject with one or two knees with symptomatic OA that are eligible to be a Fast Progressor and/or a Non Progressor**.

An eligible knee is defined as:

1.1a. Mild-moderate symptomatic OA at baseline: in the same knee, KLG 2-3 and frequent pain (pain on most days of a month in past year) at baseline.

1.1b. Medial compartment JSW>=1.5 mm (VooMCMJSW>=1.5) at baseline since at <1.5 mm knee is already close to end stage and further fast progression is less unlikely to be preventable at that point; in addition JSW measurement is less reliable when knee approaches bone on bone.

1.1c. JSN in medial compartment at baseline is equal to or worse than JSN in lateral compartment.

1.1d. JSW data at BL, 24 m and 48 m time points. (Exception: Fast Progressor knees can be missing JSW due to a TKR at 36 or 48 m.).

1.1e. Adequate radiographic positioning at BL, 24 and 48 m time points defined as VxxTPCFDS<7.0 mm and change in VxxTPCFDS<2 mm in magnitude BL to 24 m or BL to 48 m.

1.2. Subjects with only one eligible knee at baseline**:

1.2a. The contralateral knee KLG is less than or equal to the eligible knee at baseline. (e.g., subjects with a KLG 2 symptomatic eligible knee can have a KLG 0-2 symptomatic or non-symptomatic. If the eligible knee is KLG 3, then the contralataeral knee can be a KLG 0-3 symptomatic or non-symptomatic knee. The contralateral knee must have a baseline medial JSW of >=1.5 mm.

2. Subject Exclusion.

2.1 TKR in either knee at BL, 12 m or 24 m.

2.2 RA diagnosis at any visit thru 72 m (RAVISIT is 0, 1, 2, 5, 6 or 8). What about subjects with self-reported psoriatic arthritis, AS, or reactive arthritis? How many are there?

2.3 Oral Glucocorticoid use reported at >=2 visits from BL to 72 m. How many are there?

3. Classify eligible knees of eligible subjects as Fast Progressor or Non-Progressor Index knees.

3.1 Fast Progressor Index knees: JSW loss of more than 0.7 mm between BL and 24 m and remains narrowed more than 0.7 mm at 48 m or has a TKR by 48 m.

3.2 Non-Progressor Index knees: JSW loss less than 0.5 mm between BL and 24 m and remains narrowed less than 0.5 mm at 48 m. Knee does not have TKR at 36 m or 48 m and does not have lateral JSN progression through 48 m.

4. Fast Progressor Subjects.

A Fast Progressor subject has one or two Fast Progressor Index knees.

For those with one Fast Progressor Index knee the contralateral knee can be:

4.1 A Non Progressor Index knee with a KLG≤to the KLG of the progressor knee;

4.2 An ineligible knee (e.g. KLG 0-1, KLG 2-3 nonsymptomatic and KLG≤to the KLG of Progressor knee) that meets Fast Progressor JSW criteria;

4.3 An ineligible knee that does not meet Fast Progressor criteria and KLG≤to the KLG of Progressor knee; or

4.4 An ineligible knee that does not meet conditions 1.1b to 1.1e and KLG≤to the KLG of Progressor knee.

5. Non Progressor Subjects

A Non Progressor Subject has one or two Non Progressor Index knees.

If a subject has only one Non Progressor Index knee:

5.1. The contralateral knee cannot be a Fast Progressor Index knee;

5.2. If the contralateral knee is not an eligible knee, then the contralateral knee must a) have KLG≤to the KLG of Progressor knee, b) allow assessment for Fast Progression (meet conditions 1.1b. to 1.1e.) and c) have JSW loss less than 0.5 mm between BL and 24 m and remain narrowed less than 0.5 mm at 48 m, d) does not have lateral JSN progression by 48 m and e) does not have TKR at 36 m or 48 m.

Example 2. Modeling Method and Development/Validation Sample Selection

Designed to differentiate rapid radiographic and/or pain progressors from nonprogressors. This study utilized the Foundation for the NIH cohort of the OAI using biochemical biomarker data (PMID 27296323).

Development and validation on 464 (to date, estimated 600 upon completion) patients, including 299 rapid radiographic- and/or pain-progressors and 165 nonprogressors. All participants had baseline Kellegren-Lawrence radiographic grade (KLG) of 1-3 in at least one knee without a history of total knee joint replacement through 24-months. Patients with radiographic and/or pain progression by 12-months were excluded.

Case definition. Radiographic progressors had radiographic progression in the medial tibiofemoral compartment by a longitudinal loss in the minimum JSW of at least 0.7 mm from baseline to 24-month follow-up in one index knee, with persistent narrowing in the same index knee at 48 months based on radiographs obtained from a non-fluoroscopic fixed flexion protocol (Synaflexor, Synarc, Newark, Calif.). Participants with a tibial plateau rim distance of 6.5 mm at baseline, or with a change in the rim distance of >2.0 mm between baseline and follow-up were excluded due to inappropriate and/or unreliable radiographic positioning. Non-radiographic progressors were defined as those with ≤0.5 mm of JSW loss from baseline to 48 months in either knee.

Pain progressors were defined as >=9 points at 2 or more timepoints on the Western Ontario McMasters (WOMAC) pain subscale from the 24-month to 60-month pain assessment.

Controls were frequency matched with cases by age category, sex, race, and BMI category (<25, 25-27.5, 27.5-30, 30-35, and >=35 kg/m2.

DNA methylation assays, PBMC composition assessment and adjustment. Five hundred nanograms of DNA was treated with sodium bisulfite (EZ DNA methylation kit, Zymo) and loaded onto Illumina Infinium HumanMethylation850k arrays. DNA methylation data were corrected for cell count variation using frozen surrogate variable analysis via the sva package (v. 3.28.0).

Data preprocessing. Statistical analysis was performed using R (v. 3.5.0). Raw .IDAT files were processed using the ChAMP package v.2.20.1. Preprocessing and normalization were performed using Beta-Mixture Quantile (BMIQ) normalization. Beta values, defined as the fraction methylation (0-1 scale) for a particular CpG site were used for model development. The inventors excluded from analysis CpG probes located on sex chromosomes, probes with known single nucleotide polymorphisms (SNPs) with minor allele frequency of ≥5%, and probes not detected in all samples, leaving a final n=710,589 CpG sites for analysis in each sample. The simplified method eliminated the need to correct for PBMC composition and batch correction using frozen surrogate variable analysis (fsva). This method also increased the random split to 1:10, and is 10-fold validated, with an increase to 664,736 CpGs+/−gimnet models.

Modeling. Elastic-net regularized generalized linear models were developed using the glmnet package (v. 2.0-16). First, 10-fold internal cross-validation was performed during development via the cv.glmnet function, utilizing the ‘one standard error rule’ when selecting lambda values. Second, the models were tested on lockbox data not used for training (FIG. 4). Finally, model development was repeated and tested with 40 cycles of random splits of data into development and lockbox (validation) subsets. During each cycle of development, data were first randomly split into 70% development and 30% lockbox sets. Development data were then used to generate regularized cross-validated models and these models were tested on lockbox data and performance characteristics recorded. Model performance was assessed by the mean c-statistic (area under the receiver operator characteristic curve AUC-ROC), diagnostic odds ratio, accuracy, sensitivity, and specificity. The identity of DNA methylation sites (features) selected by glmnet for inclusion in each model, and the total number of sites required by each model, were recorded and compared.

Differences between the two approaches in Example 1 and 2. Smaller number of development and validation groups in the initial approach. Inclusion of both pain and radiographic progressors in the new approach vs. radiographic progressors only. It is now possible to differentiate pain vs. radiographic vs. dual progressors using a stepwise learning approach. Different/more extensive DNA methylation arrays used for the new approach. Increased cross-validation folds used in the new approach (10 vs. 7). Different development/validation ratio can also be used in the new approach (80/20 vs. 70/30). The CpG sites selected by the new modeling approach were substantially different than the original study (owing to inclusion of pain progressors and much larger number of CpG sites made available to the modeling system with the use of 850k chips).

Additional variations between Example 1 and Example 2. OAI/FNIH samples were DNA obtained from Buffy coat (peripheral blood mononuclear cells+neutrophils). A second set of sample DNA (Johnson County (JoCo)) was obtained from peripheral blood mononuclear cells (no neutrophils). The difference in initial cell type, along with differences in radiographic measurements, contribute to reduced discrimination capability of the models; however, the accuracy the models display even given these differences speak to the robustness of the process and final models. The Beta- and M-models performed equivalently in this new modeling cohort; therefore, models based on beta values (more commonly used in DNA methylation analyses) were utilized.

Johnson County (JoCo) cohort. 121 total participants, 70 progressors, 51 control nonprogressors. Definition of progression (different than previous cohorts given lack of quantitative joint space measurements). Radiographic progressors: Increase in overall radiographic grade (Kellegren-Lawrence Grade, KLG) of at least 1 from baseline to 48 months. Non-radiographic-progressors: No increase, or within-grade increase, in KLG from baseline to 48 months.

TABLE 6 Model expansion and redevelopment (FNIH-OABC cohort (n = 471), JoCo cohort (n = 121)). FNIH-OABC cohort JoCo cohort (mean ± SEM) (mean ± SEM) ROC-AUC (c-statistic)  0.94 ± 0.004 0.85 ± 0.001 Accuracy 84 ± 1% 70 ± 1%  Odds ratio 73 ± 8  — Sensitivity 81 ± 1% — Specificity 93 ± 1% —

Example 3. Peripheral Blood DNA Methylation-Based Machine Learning Models to Predict Future OA Progression

As outlined above, baseline peripheral blood cell DNA methylation patterns from a group of patients from the Osteoarthritis Initiative (OAI) and demonstrated methylation-based models distinguish future radiographic progressors from nonprogressors. In this example, the method to the FNIH OsteoArthritis Biomarkers Consortium (OABC) subcohort of the OAI that included pain-, radiographic-, and dual- (both pain and radiographic) progressors compared to nonprogressors controls was used.

Buffy coat DNA was obtained from the OAI from baseline visits of OABC patients (n=600). 500 ng of DNA was bisulfite treated and loaded onto Illumina EPIC arrays then imaged by the Clinical Genomics Center at the Oklahoma Medical Research Foundation. Raw data were extracted and Beta-Mixture Quantile (BMIQ) normalized using the Chip Analysis Methylation Pipeline (ChAMP) package. 46 samples were eliminated due to low quality or sex mismatch leaving 81 radiographic-, 91 pain-, 193 dual-, and 189 non-progressors. Elastic net-penalized generalized linear models (GLMs) were then developed. Following a 70%-development, 30%-validation data split, GLMs underwent further internal 10-fold cross validation and optimized models were tested on validation data. Model development was repeated for a total of 40 randomized data splits and mean performance calculated. Supervised ‘reduced’ models were developed by reducing the dataset to include those CpG sites selected in ≥10/40 development rounds in the any- vs. nonprogressor comparison (n=13 CpGs). An independent radiographic progressor validation cohort was obtained from the Johnston County Osteoarthritis Project (JoCo), including 89 future progressors (≥1 K/L grade worsening at 48 mo or joint replacement) and 56 nonprogressors (no- or within-grade K/L worsening). Peripheral blood mononuclear cells methylation was quantified, 33 samples were removed due to low quality. Models were also tested on DNA methylation data from our previous peripheral blood methylation publication, including 27 radiographic-only and 28 nonprogressors from the OAI cohort.

Baseline buffy coat DNA methylation patterns accurately predicted future radiographic (accuracy 87%±0.8% mean±SEM, see Table 7 for AUC-ROC c-statistic, pain (89%±0.9%), dual radiographic+pain (72%±0.7%), and ‘all’ progressors (radiographic, pain, or dual) (78%±0.4%). Intriguingly, pain-only and radiographic-only progressors were not reliably distinguished (accuracy 58%±1%). The inclusion of demographic characteristics did not alter model performance, nor the addition of baseline serum/urine analytes, nor the inclusion of methylation array batch data. Models included a mean of 13±1 CpG sites. Supervised reduced models including 13 CpG sites (cg04195161, cg22064129, cg04985016, cg12692919, cg04043957, cg08872579, cg02019955, cg01333532, cg23705082, cg05042110, cg00715363, cg01307007 and cg09239099) had similar discriminatory capability (Table 7). Despite differences in the definition of radiographic progression and the cell type input (buffy coat vs. PBMC) in the JoCo cohort, models accurately discriminated radiographic progressors from nonprogressors (81%±0.3%). Models also performed accurately when applied to our previous OAI DNA methylation dataset (80% 0.3%).

These results confirm the predictive capability of peripheral blood-based DNA methylation models in a large cohort of OA patients and confirmed these findings in two independent cohorts. These data show that a pain and structural progression share early systemic immune epigenotypes.

TABLE 7 Model performance characteristics Unsupervised ‘full’ models Supervised ‘reduced’ models Accuracy AUC-ROC Accuracy AUC-ROC Comparison groups (mean ± SEM) (mean ± SEM) (mean ± SEM) (mean ± SEM) Radiographic-only vs. 87% ± 0.8% 0.94 ± 0.004 89% ± 0.5% 0.94 ± 0.003 nonprogressor Pain-only vs. 89% ± 0.9% 0.97 ± 0.004 90% ± 0.7% 0.95 ± 0.005 nonprogressor Dual- vs. nonprogressor 72% ± 0.7% 0.79 ± 0.006 76% ± 0.6% 0.85 ± 0.005 Any 78% ± 0.4% 0.86 ± 0.004 82% ± 0.3% 0.89 ± 0.003 (pain/radiographic/dual) vs. nonprogressor Radiographic-only vs. 0.58% ± 1%    0.62 ± 0.01  n/a n/a pain-only JoCo cohort: 81% ± 0.3% 0.89 ± 0.002 radiographic-only vs. nonprogressor OAI cohort from our 80% ± 0.4% 0.89 ± 0.002 previous study: radiographic-only vs. nonprogressor

It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method, kit, reagent, or composition of the invention, and vice versa. Furthermore, compositions of the invention can be used to achieve methods of the invention.

It will be understood that particular embodiments described herein are shown by way of illustration and not as limitations of the invention. The principal features of this invention can be employed in various embodiments without departing from the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the claims.

All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.

As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. In embodiments of any of the compositions and methods provided herein, “comprising” may be replaced with “consisting essentially of” or “consisting of”. As used herein, the phrase “consisting essentially of” requires the specified integer(s) or steps as well as those that do not materially affect the character or function of the claimed invention. As used herein, the term “consisting” is used to indicate the presence of the recited integer (e.g., a feature, an element, a characteristic, a property, a method/process step or a limitation) or group of integers (e.g., feature(s), element(s), characteristic(s), propertie(s), method/process steps or limitation(s)) only.

The term “or combinations thereof” as used herein refers to all permutations and combinations of the listed items preceding the term. For example, “A, B, C, or combinations thereof” is intended to include at least one of: A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB.

Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, AB, BBC, AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.

As used herein, words of approximation such as, without limitation, “about”, “substantial” or “substantially” refers to a condition that when so modified is understood to not necessarily be absolute or perfect but would be considered close enough to those of ordinary skill in the art to warrant designating the condition as being present. The extent to which the description may vary will depend on how great a change can be instituted and still have one of ordinary skilled in the art recognize the modified feature as still having the required characteristics and capabilities of the unmodified feature. In general, but subject to the preceding discussion, a numerical value herein that is modified by a word of approximation such as “about” may vary from the stated value by at least ±1, 2, 3, 4, 5, 6, 7, 10, 12 or 15%.

Additionally, the section headings herein are provided for consistency with the suggestions under 37 CFR 1.77 or otherwise to provide organizational cues. These headings shall not limit or characterize the invention(s) set out in any claims that may issue from this disclosure. Specifically and by way of example, although the headings refer to a “Field of Invention,” such claims should not be limited by the language under this heading to describe the so-called technical field. Further, a description of technology in the “Background of the Invention” section is not to be construed as an admission that technology is prior art to any invention(s) in this disclosure. Neither is the “Summary” to be considered a characterization of the invention(s) set forth in issued claims. Furthermore, any reference in this disclosure to “invention” in the singular should not be used to argue that there is only a single point of novelty in this disclosure. Multiple inventions may be set forth according to the limitations of the multiple claims issuing from this disclosure, and such claims accordingly define the invention(s), and their equivalents, that are protected thereby. In all instances, the scope of such claims shall be considered on their own merits in light of this disclosure, but should not be constrained by the headings set forth herein.

All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

To aid the Patent Office, and any readers of any patent issued on this application in interpreting the claims appended hereto, applicants wish to note that they do not intend any of the appended claims to invoke paragraph 6 of 35 U.S.C. § 112, U.S.C. § 112 paragraph (f), or equivalent, as it exists on the date of filing hereof unless the words “means for” or “step for” are explicitly used in the particular claim.

For each of the claims, each dependent claim can depend both from the independent claim and from each of the prior dependent claims for each and every claim so long as the prior claim provides a proper antecedent basis for a claim term or element.

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What is claimed is:
 1. A method for determining whether a subject diagnosed with osteoarthritis is at increased risk for progression to severe osteoarthritis within 12-24 months, the method comprising the steps of: (a) preparing a blood sample; (b) measuring in the blood sample prepared in step (a) a level of DNA methylation; (c) comparing the DNA methylation level(s) measured in step (b) to a control blood sample level(s) of DNA methylation in a subject without osteoarthritis; and (d) identifying the subject as being at increased risk for progression to severe osteoarthritis within 12-24 months when the DNA methylation is increased by at least 2 fold as compared to the control blood level(s) of DNA methylation.
 2. The method of claim 1, wherein the blood sample comprises peripheral blood mononuclear cells or cell-free DNA.
 3. The method of claim 1, further comprising the step of preprocessing the array data by: excluding from analysis CpG probes located on sex chromosomes, probes with known single nucleotide polymorphisms (SNPs) with minor allele frequency of ≥5%, and probes not detected in all samples.
 4. The method of claim 3, wherein the control subject (i) is matched to the tested subject by at least one of: age category, sex, BMI category, ethnicity, or baseline KL radiographic grade; and (ii) does not have osteoarthritis as determined by both radiographic and symptomatic examination.
 5. The method of claim 1, wherein the control blood level of the DNA methylation is a predetermined standard.
 6. The method of claim 1, wherein the DNA methylation is determined with a 450k, or 850k array, or CpG sites associates with at least one of: an antigen presentation pathway, adenosine monophosphate kinase (AMPK) signaling pathway, or a sonic hedgehog signaling pathway, or one or more top upstream regulators identified by IPA selected from transcription factor PITX2, histone H3, histone H4, miR-141, miR-9, miR-137, bone morphogenic protein 2, a TGF-β superfamily member, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 markers selected from cg04195161, cg22064129, cg04985016, cg12692919, cg04043957, cg08872579, cg02019955, cg01333532, cg23705082, cg05042110, cg00715363, cg01307007 and cg09239099.
 7. The method of claim 1, wherein the subject is human.
 8. The method of claim 1, wherein the osteoarthritis is a knee osteoarthritis.
 9. The method of claim 8, wherein the subject has a Kellgren-Lawrence (KL) score of 1-3 in at least one knee.
 10. The method of claim 1, further comprising the step of treating the osteoarthritis wherein the treatment is at least one of acetaminophen, steroids, hyaluronic acid, nonsteroidal anti-inflammatory drugs (NSAIDs), or Duloxetine.
 11. A method for treating osteoarthritis in a subject, wherein the subject has been diagnosed with osteoarthritis but does not have severe osteoarthritis, the method comprising the steps of: (a) measuring in a blood plasma sample obtained from the subject the plasma level of DNA methylation; and (b) if the plasma level DNA methylation is increased by at least 2 fold as compared to a control plasma level(s) of the DNA methylation in a subject without osteoarthritis, administering an osteoarthritis treatment to the subject.
 12. The method of claim 11, wherein the subject has been diagnosed with knee osteoarthritis and has a Kellgren-Lawrence (KL) score of 1-3 in at least one knee.
 13. The method of claim 11, wherein the subject is human.
 14. The method of claim 11, wherein the blood plasma sample obtained from the subject has been prepared in the presence of heparin.
 15. The method of claim 11, wherein the DNA methylation is determined with a 450k, or 850k array, or CpG sites associates with at least one of: an antigen presentation pathway, adenosine monophosphate kinase (AMPK) signaling pathway, or a sonic hedgehog signaling pathway, or one or more top upstream regulators identified by IPA selected from transcription factor PITX2, histone H3, histone H4, miR-141, miR-9, miR-137, bone morphogenic protein 2, a TGF-β superfamily member, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 markers selected from cg04195161, cg22064129, cg04985016, cg12692919, cg04043957, cg08872579, cg02019955, cg01333532, cg23705082, cg05042110, cg00715363, cg01307007 and cg09239099.
 16. The method of claim 11, wherein the control blood level of the DNA methylation is a level of DNA methylation in a similarly processed blood sample from a control subject or a mean level of several control subjects.
 17. The method of claim 16, wherein the control subject (i) is matched to the tested subject by at least one of: age category, sex, BMI category, ethnicity, or baseline KL radiographic grade; and (ii) does not have osteoarthritis as determined by both radiographic and symptomatic examination.
 18. The method of claim 11, wherein the control plasma level of the DNA methylation is a predetermined standard.
 19. The method of claim 11, wherein the osteoarthritis treatment is at least one of acetaminophen, steroids, hyaluronic acid, nonsteroidal anti-inflammatory drugs (NSAIDs), or Duloxetine.
 20. A method for treating osteoarthritis in a subject, the method comprising administering an osteoarthritis treatment to a subject with elevated plasma levels of DNA methylation, wherein the subject does not have severe osteoarthritis.
 21. The method of claim 20, wherein the subject has been diagnosed with knee osteoarthritis and has a Kellgren-Lawrence (KL) score of 1-3 in at least one knee.
 22. The method of claim 20, wherein the subject is human.
 23. The method of claim 20, wherein the osteoarthritis treatment is at least one of acetaminophen, steroids, hyaluronic acid, nonsteroidal anti-inflammatory drugs (NSAIDs), or Duloxetine. 